data_8Y8X # _entry.id 8Y8X # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.404 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 8Y8X pdb_00008y8x 10.2210/pdb8y8x/pdb WWPDB D_1300045109 ? ? EMDB EMD-39063 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-03-19 ? 2 'EM metadata' 1 0 2025-03-19 ? 3 FSC 1 0 2025-03-19 ? 4 'Half map' 1 0 2025-03-19 1 5 'Half map' 1 0 2025-03-19 2 6 Image 1 0 2025-03-19 ? 7 Mask 1 0 2025-03-19 ? 8 'Primary map' 1 0 2025-03-19 ? 9 'Structure model' 1 1 2025-04-02 ? 10 FSC 1 0 2025-03-19 ? 11 'Half map' 1 0 2025-03-19 1 12 'Half map' 1 0 2025-03-19 2 13 Image 1 0 2025-03-19 ? 14 Mask 1 0 2025-03-19 ? 15 'Primary map' 1 0 2025-03-19 ? 16 'Structure model' 1 2 2025-07-02 ? 17 'EM metadata' 1 1 2025-07-02 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? 3 3 FSC repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 'Half map' repository 'Initial release' ? ? 6 6 Image repository 'Initial release' ? ? 7 7 Mask repository 'Initial release' ? ? 8 8 'Primary map' repository 'Initial release' ? ? 9 10 FSC repository 'Initial release' ? ? 10 11 'Half map' repository 'Initial release' ? ? 11 12 'Half map' repository 'Initial release' ? ? 12 13 Image repository 'Initial release' ? ? 13 14 Mask repository 'Initial release' ? ? 14 15 'Primary map' repository 'Initial release' ? ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 9 'Structure model' 'Data collection' 2 9 'Structure model' 'Database references' 3 16 'Structure model' 'Data collection' 4 17 'EM metadata' 'Data processing' 5 17 'EM metadata' 'Experimental summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 9 'Structure model' citation 2 9 'Structure model' em_admin 3 16 'Structure model' em_admin 4 16 'Structure model' em_software 5 17 'EM metadata' em_admin 6 17 'EM metadata' em_software # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 9 'Structure model' '_citation.journal_volume' 2 9 'Structure model' '_citation.page_first' 3 9 'Structure model' '_citation.page_last' 4 9 'Structure model' '_citation.pdbx_database_id_PubMed' 5 9 'Structure model' '_citation.title' 6 9 'Structure model' '_em_admin.last_update' 7 16 'Structure model' '_em_admin.last_update' 8 16 'Structure model' '_em_software.name' 9 17 'EM metadata' '_em_admin.last_update' 10 17 'EM metadata' '_em_software.name' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8Y8X _pdbx_database_status.recvd_initial_deposition_date 2024-02-06 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of GlpF with P177 deletion in POPC nanodisc' _pdbx_database_related.db_id EMD-39063 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email yoshi.cesp@tmd.ac.jp _pdbx_contact_author.name_first Yoshinori _pdbx_contact_author.name_last Fujiyoshi _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-8070-1493 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kozai, D.' 1 ? 'Suzuki, S.' 2 ? 'Kamegawa, A.' 3 ? 'Nishikawa, K.' 4 ? 'Suzuki, H.' 5 ? 'Fujiyoshi, Y.' 6 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 16 _citation.language ? _citation.page_first 2653 _citation.page_last 2653 _citation.title 'Narrowed pore conformations of aquaglyceroporins AQP3 and GlpF.' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-025-57728-3 _citation.pdbx_database_id_PubMed 40113770 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kozai, D.' 1 ? primary 'Inoue, M.' 2 ? primary 'Suzuki, S.' 3 ? primary 'Kamegawa, A.' 4 ? primary 'Nishikawa, K.' 5 ? primary 'Suzuki, H.' 6 ? primary 'Ekimoto, T.' 7 ? primary 'Ikeguchi, M.' 8 ? primary 'Fujiyoshi, Y.' 9 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Glycerol uptake facilitator protein' _entity.formula_weight 31820.100 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation P177deletion _entity.pdbx_fragment ? _entity.details '2-9 His tag 14-19 thrombin digestion site' # _entity_name_com.entity_id 1 _entity_name_com.name 'Aquaglyceroporin,Glycerol facilitator' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;MHHHHHHHHAAAGLVPRGSMSQTSTLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAG VSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNP HINFVQAFAVEMVITAILMGLILALTDDGNGVPRGLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNV AFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHLPCDICVVEEKETTTPSEQKASL ; _entity_poly.pdbx_seq_one_letter_code_can ;MHHHHHHHHAAAGLVPRGSMSQTSTLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAG VSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNP HINFVQAFAVEMVITAILMGLILALTDDGNGVPRGLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNV AFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHLPCDICVVEEKETTTPSEQKASL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 HIS n 1 3 HIS n 1 4 HIS n 1 5 HIS n 1 6 HIS n 1 7 HIS n 1 8 HIS n 1 9 HIS n 1 10 ALA n 1 11 ALA n 1 12 ALA n 1 13 GLY n 1 14 LEU n 1 15 VAL n 1 16 PRO n 1 17 ARG n 1 18 GLY n 1 19 SER n 1 20 MET n 1 21 SER n 1 22 GLN n 1 23 THR n 1 24 SER n 1 25 THR n 1 26 LEU n 1 27 LYS n 1 28 GLY n 1 29 GLN n 1 30 CYS n 1 31 ILE n 1 32 ALA n 1 33 GLU n 1 34 PHE n 1 35 LEU n 1 36 GLY n 1 37 THR n 1 38 GLY n 1 39 LEU n 1 40 LEU n 1 41 ILE n 1 42 PHE n 1 43 PHE n 1 44 GLY n 1 45 VAL n 1 46 GLY n 1 47 CYS n 1 48 VAL n 1 49 ALA n 1 50 ALA n 1 51 LEU n 1 52 LYS n 1 53 VAL n 1 54 ALA n 1 55 GLY n 1 56 ALA n 1 57 SER n 1 58 PHE n 1 59 GLY n 1 60 GLN n 1 61 TRP n 1 62 GLU n 1 63 ILE n 1 64 SER n 1 65 VAL n 1 66 ILE n 1 67 TRP n 1 68 GLY n 1 69 LEU n 1 70 GLY n 1 71 VAL n 1 72 ALA n 1 73 MET n 1 74 ALA n 1 75 ILE n 1 76 TYR n 1 77 LEU n 1 78 THR n 1 79 ALA n 1 80 GLY n 1 81 VAL n 1 82 SER n 1 83 GLY n 1 84 ALA n 1 85 HIS n 1 86 LEU n 1 87 ASN n 1 88 PRO n 1 89 ALA n 1 90 VAL n 1 91 THR n 1 92 ILE n 1 93 ALA n 1 94 LEU n 1 95 TRP n 1 96 LEU n 1 97 PHE n 1 98 ALA n 1 99 CYS n 1 100 PHE n 1 101 ASP n 1 102 LYS n 1 103 ARG n 1 104 LYS n 1 105 VAL n 1 106 ILE n 1 107 PRO n 1 108 PHE n 1 109 ILE n 1 110 VAL n 1 111 SER n 1 112 GLN n 1 113 VAL n 1 114 ALA n 1 115 GLY n 1 116 ALA n 1 117 PHE n 1 118 CYS n 1 119 ALA n 1 120 ALA n 1 121 ALA n 1 122 LEU n 1 123 VAL n 1 124 TYR n 1 125 GLY n 1 126 LEU n 1 127 TYR n 1 128 TYR n 1 129 ASN n 1 130 LEU n 1 131 PHE n 1 132 PHE n 1 133 ASP n 1 134 PHE n 1 135 GLU n 1 136 GLN n 1 137 THR n 1 138 HIS n 1 139 HIS n 1 140 ILE n 1 141 VAL n 1 142 ARG n 1 143 GLY n 1 144 SER n 1 145 VAL n 1 146 GLU n 1 147 SER n 1 148 VAL n 1 149 ASP n 1 150 LEU n 1 151 ALA n 1 152 GLY n 1 153 THR n 1 154 PHE n 1 155 SER n 1 156 THR n 1 157 TYR n 1 158 PRO n 1 159 ASN n 1 160 PRO n 1 161 HIS n 1 162 ILE n 1 163 ASN n 1 164 PHE n 1 165 VAL n 1 166 GLN n 1 167 ALA n 1 168 PHE n 1 169 ALA n 1 170 VAL n 1 171 GLU n 1 172 MET n 1 173 VAL n 1 174 ILE n 1 175 THR n 1 176 ALA n 1 177 ILE n 1 178 LEU n 1 179 MET n 1 180 GLY n 1 181 LEU n 1 182 ILE n 1 183 LEU n 1 184 ALA n 1 185 LEU n 1 186 THR n 1 187 ASP n 1 188 ASP n 1 189 GLY n 1 190 ASN n 1 191 GLY n 1 192 VAL n 1 193 PRO n 1 194 ARG n 1 195 GLY n 1 196 LEU n 1 197 ALA n 1 198 PRO n 1 199 LEU n 1 200 LEU n 1 201 ILE n 1 202 GLY n 1 203 LEU n 1 204 LEU n 1 205 ILE n 1 206 ALA n 1 207 VAL n 1 208 ILE n 1 209 GLY n 1 210 ALA n 1 211 SER n 1 212 MET n 1 213 GLY n 1 214 PRO n 1 215 LEU n 1 216 THR n 1 217 GLY n 1 218 PHE n 1 219 ALA n 1 220 MET n 1 221 ASN n 1 222 PRO n 1 223 ALA n 1 224 ARG n 1 225 ASP n 1 226 PHE n 1 227 GLY n 1 228 PRO n 1 229 LYS n 1 230 VAL n 1 231 PHE n 1 232 ALA n 1 233 TRP n 1 234 LEU n 1 235 ALA n 1 236 GLY n 1 237 TRP n 1 238 GLY n 1 239 ASN n 1 240 VAL n 1 241 ALA n 1 242 PHE n 1 243 THR n 1 244 GLY n 1 245 GLY n 1 246 ARG n 1 247 ASP n 1 248 ILE n 1 249 PRO n 1 250 TYR n 1 251 PHE n 1 252 LEU n 1 253 VAL n 1 254 PRO n 1 255 LEU n 1 256 PHE n 1 257 GLY n 1 258 PRO n 1 259 ILE n 1 260 VAL n 1 261 GLY n 1 262 ALA n 1 263 ILE n 1 264 VAL n 1 265 GLY n 1 266 ALA n 1 267 PHE n 1 268 ALA n 1 269 TYR n 1 270 ARG n 1 271 LYS n 1 272 LEU n 1 273 ILE n 1 274 GLY n 1 275 ARG n 1 276 HIS n 1 277 LEU n 1 278 PRO n 1 279 CYS n 1 280 ASP n 1 281 ILE n 1 282 CYS n 1 283 VAL n 1 284 VAL n 1 285 GLU n 1 286 GLU n 1 287 LYS n 1 288 GLU n 1 289 THR n 1 290 THR n 1 291 THR n 1 292 PRO n 1 293 SER n 1 294 GLU n 1 295 GLN n 1 296 LYS n 1 297 ALA n 1 298 SER n 1 299 LEU n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 299 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'glpF, b3927, JW3898' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 562 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Spodoptera frugiperda' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 7108 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 -18 ? ? ? A . n A 1 2 HIS 2 -17 ? ? ? A . n A 1 3 HIS 3 -16 ? ? ? A . n A 1 4 HIS 4 -15 ? ? ? A . n A 1 5 HIS 5 -14 ? ? ? A . n A 1 6 HIS 6 -13 ? ? ? A . n A 1 7 HIS 7 -12 ? ? ? A . n A 1 8 HIS 8 -11 ? ? ? A . n A 1 9 HIS 9 -10 ? ? ? A . n A 1 10 ALA 10 -9 ? ? ? A . n A 1 11 ALA 11 -8 ? ? ? A . n A 1 12 ALA 12 -7 ? ? ? A . n A 1 13 GLY 13 -6 ? ? ? A . n A 1 14 LEU 14 -5 ? ? ? A . n A 1 15 VAL 15 -4 ? ? ? A . n A 1 16 PRO 16 -3 ? ? ? A . n A 1 17 ARG 17 -2 ? ? ? A . n A 1 18 GLY 18 -1 ? ? ? A . n A 1 19 SER 19 0 ? ? ? A . n A 1 20 MET 20 1 ? ? ? A . n A 1 21 SER 21 2 ? ? ? A . n A 1 22 GLN 22 3 ? ? ? A . n A 1 23 THR 23 4 ? ? ? A . n A 1 24 SER 24 5 5 SER SER A . n A 1 25 THR 25 6 6 THR THR A . n A 1 26 LEU 26 7 7 LEU LEU A . n A 1 27 LYS 27 8 8 LYS LYS A . n A 1 28 GLY 28 9 9 GLY GLY A . n A 1 29 GLN 29 10 10 GLN GLN A . n A 1 30 CYS 30 11 11 CYS CYS A . n A 1 31 ILE 31 12 12 ILE ILE A . n A 1 32 ALA 32 13 13 ALA ALA A . n A 1 33 GLU 33 14 14 GLU GLU A . n A 1 34 PHE 34 15 15 PHE PHE A . n A 1 35 LEU 35 16 16 LEU LEU A . n A 1 36 GLY 36 17 17 GLY GLY A . n A 1 37 THR 37 18 18 THR THR A . n A 1 38 GLY 38 19 19 GLY GLY A . n A 1 39 LEU 39 20 20 LEU LEU A . n A 1 40 LEU 40 21 21 LEU LEU A . n A 1 41 ILE 41 22 22 ILE ILE A . n A 1 42 PHE 42 23 23 PHE PHE A . n A 1 43 PHE 43 24 24 PHE PHE A . n A 1 44 GLY 44 25 25 GLY GLY A . n A 1 45 VAL 45 26 26 VAL VAL A . n A 1 46 GLY 46 27 27 GLY GLY A . n A 1 47 CYS 47 28 28 CYS CYS A . n A 1 48 VAL 48 29 29 VAL VAL A . n A 1 49 ALA 49 30 30 ALA ALA A . n A 1 50 ALA 50 31 31 ALA ALA A . n A 1 51 LEU 51 32 32 LEU LEU A . n A 1 52 LYS 52 33 33 LYS LYS A . n A 1 53 VAL 53 34 34 VAL VAL A . n A 1 54 ALA 54 35 35 ALA ALA A . n A 1 55 GLY 55 36 36 GLY GLY A . n A 1 56 ALA 56 37 37 ALA ALA A . n A 1 57 SER 57 38 38 SER SER A . n A 1 58 PHE 58 39 39 PHE PHE A . n A 1 59 GLY 59 40 40 GLY GLY A . n A 1 60 GLN 60 41 41 GLN GLN A . n A 1 61 TRP 61 42 42 TRP TRP A . n A 1 62 GLU 62 43 43 GLU GLU A . n A 1 63 ILE 63 44 44 ILE ILE A . n A 1 64 SER 64 45 45 SER SER A . n A 1 65 VAL 65 46 46 VAL VAL A . n A 1 66 ILE 66 47 47 ILE ILE A . n A 1 67 TRP 67 48 48 TRP TRP A . n A 1 68 GLY 68 49 49 GLY GLY A . n A 1 69 LEU 69 50 50 LEU LEU A . n A 1 70 GLY 70 51 51 GLY GLY A . n A 1 71 VAL 71 52 52 VAL VAL A . n A 1 72 ALA 72 53 53 ALA ALA A . n A 1 73 MET 73 54 54 MET MET A . n A 1 74 ALA 74 55 55 ALA ALA A . n A 1 75 ILE 75 56 56 ILE ILE A . n A 1 76 TYR 76 57 57 TYR TYR A . n A 1 77 LEU 77 58 58 LEU LEU A . n A 1 78 THR 78 59 59 THR THR A . n A 1 79 ALA 79 60 60 ALA ALA A . n A 1 80 GLY 80 61 61 GLY GLY A . n A 1 81 VAL 81 62 62 VAL VAL A . n A 1 82 SER 82 63 63 SER SER A . n A 1 83 GLY 83 64 64 GLY GLY A . n A 1 84 ALA 84 65 65 ALA ALA A . n A 1 85 HIS 85 66 66 HIS HIS A . n A 1 86 LEU 86 67 67 LEU LEU A . n A 1 87 ASN 87 68 68 ASN ASN A . n A 1 88 PRO 88 69 69 PRO PRO A . n A 1 89 ALA 89 70 70 ALA ALA A . n A 1 90 VAL 90 71 71 VAL VAL A . n A 1 91 THR 91 72 72 THR THR A . n A 1 92 ILE 92 73 73 ILE ILE A . n A 1 93 ALA 93 74 74 ALA ALA A . n A 1 94 LEU 94 75 75 LEU LEU A . n A 1 95 TRP 95 76 76 TRP TRP A . n A 1 96 LEU 96 77 77 LEU LEU A . n A 1 97 PHE 97 78 78 PHE PHE A . n A 1 98 ALA 98 79 79 ALA ALA A . n A 1 99 CYS 99 80 80 CYS CYS A . n A 1 100 PHE 100 81 81 PHE PHE A . n A 1 101 ASP 101 82 82 ASP ASP A . n A 1 102 LYS 102 83 83 LYS LYS A . n A 1 103 ARG 103 84 84 ARG ARG A . n A 1 104 LYS 104 85 85 LYS LYS A . n A 1 105 VAL 105 86 86 VAL VAL A . n A 1 106 ILE 106 87 87 ILE ILE A . n A 1 107 PRO 107 88 88 PRO PRO A . n A 1 108 PHE 108 89 89 PHE PHE A . n A 1 109 ILE 109 90 90 ILE ILE A . n A 1 110 VAL 110 91 91 VAL VAL A . n A 1 111 SER 111 92 92 SER SER A . n A 1 112 GLN 112 93 93 GLN GLN A . n A 1 113 VAL 113 94 94 VAL VAL A . n A 1 114 ALA 114 95 95 ALA ALA A . n A 1 115 GLY 115 96 96 GLY GLY A . n A 1 116 ALA 116 97 97 ALA ALA A . n A 1 117 PHE 117 98 98 PHE PHE A . n A 1 118 CYS 118 99 99 CYS CYS A . n A 1 119 ALA 119 100 100 ALA ALA A . n A 1 120 ALA 120 101 101 ALA ALA A . n A 1 121 ALA 121 102 102 ALA ALA A . n A 1 122 LEU 122 103 103 LEU LEU A . n A 1 123 VAL 123 104 104 VAL VAL A . n A 1 124 TYR 124 105 105 TYR TYR A . n A 1 125 GLY 125 106 106 GLY GLY A . n A 1 126 LEU 126 107 107 LEU LEU A . n A 1 127 TYR 127 108 108 TYR TYR A . n A 1 128 TYR 128 109 109 TYR TYR A . n A 1 129 ASN 129 110 110 ASN ASN A . n A 1 130 LEU 130 111 111 LEU LEU A . n A 1 131 PHE 131 112 112 PHE PHE A . n A 1 132 PHE 132 113 113 PHE PHE A . n A 1 133 ASP 133 114 114 ASP ASP A . n A 1 134 PHE 134 115 115 PHE PHE A . n A 1 135 GLU 135 116 116 GLU GLU A . n A 1 136 GLN 136 117 117 GLN GLN A . n A 1 137 THR 137 118 118 THR THR A . n A 1 138 HIS 138 119 119 HIS HIS A . n A 1 139 HIS 139 120 120 HIS HIS A . n A 1 140 ILE 140 121 121 ILE ILE A . n A 1 141 VAL 141 122 122 VAL VAL A . n A 1 142 ARG 142 123 123 ARG ARG A . n A 1 143 GLY 143 124 124 GLY GLY A . n A 1 144 SER 144 125 125 SER SER A . n A 1 145 VAL 145 126 126 VAL VAL A . n A 1 146 GLU 146 127 127 GLU GLU A . n A 1 147 SER 147 128 128 SER SER A . n A 1 148 VAL 148 129 129 VAL VAL A . n A 1 149 ASP 149 130 130 ASP ASP A . n A 1 150 LEU 150 131 131 LEU LEU A . n A 1 151 ALA 151 132 132 ALA ALA A . n A 1 152 GLY 152 133 133 GLY GLY A . n A 1 153 THR 153 134 134 THR THR A . n A 1 154 PHE 154 135 135 PHE PHE A . n A 1 155 SER 155 136 136 SER SER A . n A 1 156 THR 156 137 137 THR THR A . n A 1 157 TYR 157 138 138 TYR TYR A . n A 1 158 PRO 158 139 139 PRO PRO A . n A 1 159 ASN 159 140 140 ASN ASN A . n A 1 160 PRO 160 141 141 PRO PRO A . n A 1 161 HIS 161 142 142 HIS HIS A . n A 1 162 ILE 162 143 143 ILE ILE A . n A 1 163 ASN 163 144 144 ASN ASN A . n A 1 164 PHE 164 145 145 PHE PHE A . n A 1 165 VAL 165 146 146 VAL VAL A . n A 1 166 GLN 166 147 147 GLN GLN A . n A 1 167 ALA 167 148 148 ALA ALA A . n A 1 168 PHE 168 149 149 PHE PHE A . n A 1 169 ALA 169 150 150 ALA ALA A . n A 1 170 VAL 170 151 151 VAL VAL A . n A 1 171 GLU 171 152 152 GLU GLU A . n A 1 172 MET 172 153 153 MET MET A . n A 1 173 VAL 173 154 154 VAL VAL A . n A 1 174 ILE 174 155 155 ILE ILE A . n A 1 175 THR 175 156 156 THR THR A . n A 1 176 ALA 176 157 157 ALA ALA A . n A 1 177 ILE 177 158 158 ILE ILE A . n A 1 178 LEU 178 159 159 LEU LEU A . n A 1 179 MET 179 160 160 MET MET A . n A 1 180 GLY 180 161 161 GLY GLY A . n A 1 181 LEU 181 162 162 LEU LEU A . n A 1 182 ILE 182 163 163 ILE ILE A . n A 1 183 LEU 183 164 164 LEU LEU A . n A 1 184 ALA 184 165 165 ALA ALA A . n A 1 185 LEU 185 166 166 LEU LEU A . n A 1 186 THR 186 167 167 THR THR A . n A 1 187 ASP 187 168 168 ASP ASP A . n A 1 188 ASP 188 169 169 ASP ASP A . n A 1 189 GLY 189 170 170 GLY GLY A . n A 1 190 ASN 190 171 171 ASN ASN A . n A 1 191 GLY 191 172 172 GLY GLY A . n A 1 192 VAL 192 173 173 VAL VAL A . n A 1 193 PRO 193 174 174 PRO PRO A . n A 1 194 ARG 194 175 175 ARG ARG A . n A 1 195 GLY 195 176 176 GLY GLY A . n A 1 196 LEU 196 177 177 LEU LEU A . n A 1 197 ALA 197 178 178 ALA ALA A . n A 1 198 PRO 198 179 179 PRO PRO A . n A 1 199 LEU 199 180 180 LEU LEU A . n A 1 200 LEU 200 181 181 LEU LEU A . n A 1 201 ILE 201 182 182 ILE ILE A . n A 1 202 GLY 202 183 183 GLY GLY A . n A 1 203 LEU 203 184 184 LEU LEU A . n A 1 204 LEU 204 185 185 LEU LEU A . n A 1 205 ILE 205 186 186 ILE ILE A . n A 1 206 ALA 206 187 187 ALA ALA A . n A 1 207 VAL 207 188 188 VAL VAL A . n A 1 208 ILE 208 189 189 ILE ILE A . n A 1 209 GLY 209 190 190 GLY GLY A . n A 1 210 ALA 210 191 191 ALA ALA A . n A 1 211 SER 211 192 192 SER SER A . n A 1 212 MET 212 193 193 MET MET A . n A 1 213 GLY 213 194 194 GLY GLY A . n A 1 214 PRO 214 195 195 PRO PRO A . n A 1 215 LEU 215 196 196 LEU LEU A . n A 1 216 THR 216 197 197 THR THR A . n A 1 217 GLY 217 198 198 GLY GLY A . n A 1 218 PHE 218 199 199 PHE PHE A . n A 1 219 ALA 219 200 200 ALA ALA A . n A 1 220 MET 220 201 201 MET MET A . n A 1 221 ASN 221 202 202 ASN ASN A . n A 1 222 PRO 222 203 203 PRO PRO A . n A 1 223 ALA 223 204 204 ALA ALA A . n A 1 224 ARG 224 205 205 ARG ARG A . n A 1 225 ASP 225 206 206 ASP ASP A . n A 1 226 PHE 226 207 207 PHE PHE A . n A 1 227 GLY 227 208 208 GLY GLY A . n A 1 228 PRO 228 209 209 PRO PRO A . n A 1 229 LYS 229 210 210 LYS LYS A . n A 1 230 VAL 230 211 211 VAL VAL A . n A 1 231 PHE 231 212 212 PHE PHE A . n A 1 232 ALA 232 213 213 ALA ALA A . n A 1 233 TRP 233 214 214 TRP TRP A . n A 1 234 LEU 234 215 215 LEU LEU A . n A 1 235 ALA 235 216 216 ALA ALA A . n A 1 236 GLY 236 217 217 GLY GLY A . n A 1 237 TRP 237 218 218 TRP TRP A . n A 1 238 GLY 238 219 219 GLY GLY A . n A 1 239 ASN 239 220 220 ASN ASN A . n A 1 240 VAL 240 221 221 VAL VAL A . n A 1 241 ALA 241 222 222 ALA ALA A . n A 1 242 PHE 242 223 223 PHE PHE A . n A 1 243 THR 243 224 224 THR THR A . n A 1 244 GLY 244 225 225 GLY GLY A . n A 1 245 GLY 245 226 226 GLY GLY A . n A 1 246 ARG 246 227 227 ARG ARG A . n A 1 247 ASP 247 228 228 ASP ASP A . n A 1 248 ILE 248 229 229 ILE ILE A . n A 1 249 PRO 249 230 230 PRO PRO A . n A 1 250 TYR 250 231 231 TYR TYR A . n A 1 251 PHE 251 232 232 PHE PHE A . n A 1 252 LEU 252 233 233 LEU LEU A . n A 1 253 VAL 253 234 234 VAL VAL A . n A 1 254 PRO 254 235 235 PRO PRO A . n A 1 255 LEU 255 236 236 LEU LEU A . n A 1 256 PHE 256 237 237 PHE PHE A . n A 1 257 GLY 257 238 238 GLY GLY A . n A 1 258 PRO 258 239 239 PRO PRO A . n A 1 259 ILE 259 240 240 ILE ILE A . n A 1 260 VAL 260 241 241 VAL VAL A . n A 1 261 GLY 261 242 242 GLY GLY A . n A 1 262 ALA 262 243 243 ALA ALA A . n A 1 263 ILE 263 244 244 ILE ILE A . n A 1 264 VAL 264 245 245 VAL VAL A . n A 1 265 GLY 265 246 246 GLY GLY A . n A 1 266 ALA 266 247 247 ALA ALA A . n A 1 267 PHE 267 248 248 PHE PHE A . n A 1 268 ALA 268 249 249 ALA ALA A . n A 1 269 TYR 269 250 250 TYR TYR A . n A 1 270 ARG 270 251 251 ARG ARG A . n A 1 271 LYS 271 252 252 LYS LYS A . n A 1 272 LEU 272 253 253 LEU LEU A . n A 1 273 ILE 273 254 254 ILE ILE A . n A 1 274 GLY 274 255 255 GLY GLY A . n A 1 275 ARG 275 256 ? ? ? A . n A 1 276 HIS 276 257 ? ? ? A . n A 1 277 LEU 277 258 ? ? ? A . n A 1 278 PRO 278 259 ? ? ? A . n A 1 279 CYS 279 260 ? ? ? A . n A 1 280 ASP 280 261 ? ? ? A . n A 1 281 ILE 281 262 ? ? ? A . n A 1 282 CYS 282 263 ? ? ? A . n A 1 283 VAL 283 264 ? ? ? A . n A 1 284 VAL 284 265 ? ? ? A . n A 1 285 GLU 285 266 ? ? ? A . n A 1 286 GLU 286 267 ? ? ? A . n A 1 287 LYS 287 268 ? ? ? A . n A 1 288 GLU 288 269 ? ? ? A . n A 1 289 THR 289 270 ? ? ? A . n A 1 290 THR 290 271 ? ? ? A . n A 1 291 THR 291 272 ? ? ? A . n A 1 292 PRO 292 273 ? ? ? A . n A 1 293 SER 293 274 ? ? ? A . n A 1 294 GLU 294 275 ? ? ? A . n A 1 295 GLN 295 276 ? ? ? A . n A 1 296 LYS 296 277 ? ? ? A . n A 1 297 ALA 297 278 ? ? ? A . n A 1 298 SER 298 279 ? ? ? A . n A 1 299 LEU 299 280 ? ? ? A . n # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8Y8X _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8Y8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8Y8X _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 8Y8X _refine.pdbx_diffrn_id ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high . _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.002 ? 7696 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.390 ? 10500 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 5.022 ? 1069 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.037 ? 1208 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.004 ? 1316 ? f_plane_restr ? ? # loop_ _struct_ncs_oper.id _struct_ncs_oper.code _struct_ncs_oper.details _struct_ncs_oper.matrix[1][1] _struct_ncs_oper.matrix[1][2] _struct_ncs_oper.matrix[1][3] _struct_ncs_oper.matrix[2][1] _struct_ncs_oper.matrix[2][2] _struct_ncs_oper.matrix[2][3] _struct_ncs_oper.matrix[3][1] _struct_ncs_oper.matrix[3][2] _struct_ncs_oper.matrix[3][3] _struct_ncs_oper.vector[1] _struct_ncs_oper.vector[2] _struct_ncs_oper.vector[3] 2 generate ? 0.000000 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 146.73000 0.00000 0.00000 3 generate ? -1.000000 -0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 1.000000 146.73000 146.73000 0.00000 4 generate ? -0.000000 1.000000 0.000000 -1.000000 -0.000000 0.000000 0.000000 0.000000 1.000000 0.00000 146.73000 0.00000 # _struct.entry_id 8Y8X _struct.title 'Cryo-EM structure of GlpF with P177 deletion in POPC nanodisc' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8Y8X _struct_keywords.text 'water channel, aquaporin, aquaglyceroporin, glycerol, MEMBRANE PROTEIN' _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code GLPF_ECOLI _struct_ref.pdbx_db_accession P0AER0 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSQTSTLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFAC FDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILM GLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGP IVGAIVGAFAYRKLIGRHLPCDICVVEEKETTTPSEQKASL ; _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8Y8X _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 20 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 299 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0AER0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 281 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 280 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 8Y8X MET A 1 ? UNP P0AER0 ? ? 'initiating methionine' -18 1 1 8Y8X HIS A 2 ? UNP P0AER0 ? ? 'expression tag' -17 2 1 8Y8X HIS A 3 ? UNP P0AER0 ? ? 'expression tag' -16 3 1 8Y8X HIS A 4 ? UNP P0AER0 ? ? 'expression tag' -15 4 1 8Y8X HIS A 5 ? UNP P0AER0 ? ? 'expression tag' -14 5 1 8Y8X HIS A 6 ? UNP P0AER0 ? ? 'expression tag' -13 6 1 8Y8X HIS A 7 ? UNP P0AER0 ? ? 'expression tag' -12 7 1 8Y8X HIS A 8 ? UNP P0AER0 ? ? 'expression tag' -11 8 1 8Y8X HIS A 9 ? UNP P0AER0 ? ? 'expression tag' -10 9 1 8Y8X ALA A 10 ? UNP P0AER0 ? ? 'expression tag' -9 10 1 8Y8X ALA A 11 ? UNP P0AER0 ? ? 'expression tag' -8 11 1 8Y8X ALA A 12 ? UNP P0AER0 ? ? 'expression tag' -7 12 1 8Y8X GLY A 13 ? UNP P0AER0 ? ? 'expression tag' -6 13 1 8Y8X LEU A 14 ? UNP P0AER0 ? ? 'expression tag' -5 14 1 8Y8X VAL A 15 ? UNP P0AER0 ? ? 'expression tag' -4 15 1 8Y8X PRO A 16 ? UNP P0AER0 ? ? 'expression tag' -3 16 1 8Y8X ARG A 17 ? UNP P0AER0 ? ? 'expression tag' -2 17 1 8Y8X GLY A 18 ? UNP P0AER0 ? ? 'expression tag' -1 18 1 8Y8X SER A 19 ? UNP P0AER0 ? ? 'expression tag' 0 19 1 8Y8X ? A ? ? UNP P0AER0 PRO 177 deletion ? 20 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'complete point assembly' ? tetrameric 4 2 'point asymmetric unit' ? monomeric 1 3 'point asymmetric unit, std point frame' ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-4)' A 2 1 A 3 P A # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] P 'transform to point frame' ? ? -0.99906759 0.04317352 0.00000000 70.12917 -0.04317352 -0.99906759 0.00000000 76.46402 0.00000000 0.00000000 1.00000000 -82.34740 1 'identity operation' 1_555 x,y,z 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 2 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 146.73000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 3 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 146.73000 0.00000000 -1.00000000 0.00000000 146.73000 0.00000000 0.00000000 1.00000000 0.00000 4 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 -1.00000000 0.00000000 0.00000000 146.73000 0.00000000 0.00000000 1.00000000 0.00000 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 THR A 25 ? ALA A 54 ? THR A 6 ALA A 35 1 ? 30 HELX_P HELX_P2 AA2 GLY A 59 ? GLY A 83 ? GLY A 40 GLY A 64 1 ? 25 HELX_P HELX_P3 AA3 ASN A 87 ? ALA A 98 ? ASN A 68 ALA A 79 1 ? 12 HELX_P HELX_P4 AA4 ASP A 101 ? ARG A 103 ? ASP A 82 ARG A 84 5 ? 3 HELX_P HELX_P5 AA5 LYS A 104 ? TYR A 127 ? LYS A 85 TYR A 108 1 ? 24 HELX_P HELX_P6 AA6 TYR A 127 ? HIS A 139 ? TYR A 108 HIS A 120 1 ? 13 HELX_P HELX_P7 AA7 SER A 144 ? GLU A 146 ? SER A 125 GLU A 127 5 ? 3 HELX_P HELX_P8 AA8 SER A 147 ? GLY A 152 ? SER A 128 GLY A 133 1 ? 6 HELX_P HELX_P9 AA9 ASN A 163 ? THR A 186 ? ASN A 144 THR A 167 1 ? 24 HELX_P HELX_P10 AB1 LEU A 196 ? GLY A 217 ? LEU A 177 GLY A 198 1 ? 22 HELX_P HELX_P11 AB2 ASN A 221 ? GLY A 236 ? ASN A 202 GLY A 217 1 ? 16 HELX_P HELX_P12 AB3 ASN A 239 ? GLY A 244 ? ASN A 220 GLY A 225 1 ? 6 HELX_P HELX_P13 AB4 PHE A 251 ? ILE A 273 ? PHE A 232 ILE A 254 1 ? 23 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _pdbx_entry_details.entry_id 8Y8X _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 VAL A 62 ? ? -97.36 -60.79 2 1 LEU A 67 ? ? 57.40 19.14 3 1 PHE A 199 ? ? 37.37 57.52 4 1 MET A 201 ? ? 59.79 9.05 # _pdbx_point_symmetry.entry_id 8Y8X _pdbx_point_symmetry.Schoenflies_symbol C _pdbx_point_symmetry.circular_symmetry 4 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 8Y8X _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 8Y8X _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 2.26 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 462907 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7.5 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'Tetramer of GlpF with P177 deletion in POPC nanodisc' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 8Y8X _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'JEOL CRYO ARM 300' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 500 _em_imaging.nominal_defocus_max 2500 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 8Y8X _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 8Y8X _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # _em_single_particle_entity.entry_id 8Y8X _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry C4 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A MET -18 ? A MET 1 2 1 Y 1 A HIS -17 ? A HIS 2 3 1 Y 1 A HIS -16 ? A HIS 3 4 1 Y 1 A HIS -15 ? A HIS 4 5 1 Y 1 A HIS -14 ? A HIS 5 6 1 Y 1 A HIS -13 ? A HIS 6 7 1 Y 1 A HIS -12 ? A HIS 7 8 1 Y 1 A HIS -11 ? A HIS 8 9 1 Y 1 A HIS -10 ? A HIS 9 10 1 Y 1 A ALA -9 ? A ALA 10 11 1 Y 1 A ALA -8 ? A ALA 11 12 1 Y 1 A ALA -7 ? A ALA 12 13 1 Y 1 A GLY -6 ? A GLY 13 14 1 Y 1 A LEU -5 ? A LEU 14 15 1 Y 1 A VAL -4 ? A VAL 15 16 1 Y 1 A PRO -3 ? A PRO 16 17 1 Y 1 A ARG -2 ? A ARG 17 18 1 Y 1 A GLY -1 ? A GLY 18 19 1 Y 1 A SER 0 ? A SER 19 20 1 Y 1 A MET 1 ? A MET 20 21 1 Y 1 A SER 2 ? A SER 21 22 1 Y 1 A GLN 3 ? A GLN 22 23 1 Y 1 A THR 4 ? A THR 23 24 1 Y 1 A ARG 256 ? A ARG 275 25 1 Y 1 A HIS 257 ? A HIS 276 26 1 Y 1 A LEU 258 ? A LEU 277 27 1 Y 1 A PRO 259 ? A PRO 278 28 1 Y 1 A CYS 260 ? A CYS 279 29 1 Y 1 A ASP 261 ? A ASP 280 30 1 Y 1 A ILE 262 ? A ILE 281 31 1 Y 1 A CYS 263 ? A CYS 282 32 1 Y 1 A VAL 264 ? A VAL 283 33 1 Y 1 A VAL 265 ? A VAL 284 34 1 Y 1 A GLU 266 ? A GLU 285 35 1 Y 1 A GLU 267 ? A GLU 286 36 1 Y 1 A LYS 268 ? A LYS 287 37 1 Y 1 A GLU 269 ? A GLU 288 38 1 Y 1 A THR 270 ? A THR 289 39 1 Y 1 A THR 271 ? A THR 290 40 1 Y 1 A THR 272 ? A THR 291 41 1 Y 1 A PRO 273 ? A PRO 292 42 1 Y 1 A SER 274 ? A SER 293 43 1 Y 1 A GLU 275 ? A GLU 294 44 1 Y 1 A GLN 276 ? A GLN 295 45 1 Y 1 A LYS 277 ? A LYS 296 46 1 Y 1 A ALA 278 ? A ALA 297 47 1 Y 1 A SER 279 ? A SER 298 48 1 Y 1 A LEU 280 ? A LEU 299 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CYS N N N N 74 CYS CA C N R 75 CYS C C N N 76 CYS O O N N 77 CYS CB C N N 78 CYS SG S N N 79 CYS OXT O N N 80 CYS H H N N 81 CYS H2 H N N 82 CYS HA H N N 83 CYS HB2 H N N 84 CYS HB3 H N N 85 CYS HG H N N 86 CYS HXT H N N 87 GLN N N N N 88 GLN CA C N S 89 GLN C C N N 90 GLN O O N N 91 GLN CB C N N 92 GLN CG C N N 93 GLN CD C N N 94 GLN OE1 O N N 95 GLN NE2 N N N 96 GLN OXT O N N 97 GLN H H N N 98 GLN H2 H N N 99 GLN HA H N N 100 GLN HB2 H N N 101 GLN HB3 H N N 102 GLN HG2 H N N 103 GLN HG3 H N N 104 GLN HE21 H N N 105 GLN HE22 H N N 106 GLN HXT H N N 107 GLU N N N N 108 GLU CA C N S 109 GLU C C N N 110 GLU O O N N 111 GLU CB C N N 112 GLU CG C N N 113 GLU CD C N N 114 GLU OE1 O N N 115 GLU OE2 O N N 116 GLU OXT O N N 117 GLU H H N N 118 GLU H2 H N N 119 GLU HA H N N 120 GLU HB2 H N N 121 GLU HB3 H N N 122 GLU HG2 H N N 123 GLU HG3 H N N 124 GLU HE2 H N N 125 GLU HXT H N N 126 GLY N N N N 127 GLY CA C N N 128 GLY C C N N 129 GLY O O N N 130 GLY OXT O N N 131 GLY H H N N 132 GLY H2 H N N 133 GLY HA2 H N N 134 GLY HA3 H N N 135 GLY HXT H N N 136 HIS N N N N 137 HIS CA C N S 138 HIS C C N N 139 HIS O O N N 140 HIS CB C N N 141 HIS CG C Y N 142 HIS ND1 N Y N 143 HIS CD2 C Y N 144 HIS CE1 C Y N 145 HIS NE2 N Y N 146 HIS OXT O N N 147 HIS H H N N 148 HIS H2 H N N 149 HIS HA H N N 150 HIS HB2 H N N 151 HIS HB3 H N N 152 HIS HD1 H N N 153 HIS HD2 H N N 154 HIS HE1 H N N 155 HIS HE2 H N N 156 HIS HXT H N N 157 ILE N N N N 158 ILE CA C N S 159 ILE C C N N 160 ILE O O N N 161 ILE CB C N S 162 ILE CG1 C N N 163 ILE CG2 C N N 164 ILE CD1 C N N 165 ILE OXT O N N 166 ILE H H N N 167 ILE H2 H N N 168 ILE HA H N N 169 ILE HB H N N 170 ILE HG12 H N N 171 ILE HG13 H N N 172 ILE HG21 H N N 173 ILE HG22 H N N 174 ILE HG23 H N N 175 ILE HD11 H N N 176 ILE HD12 H N N 177 ILE HD13 H N N 178 ILE HXT H N N 179 LEU N N N N 180 LEU CA C N S 181 LEU C C N N 182 LEU O O N N 183 LEU CB C N N 184 LEU CG C N N 185 LEU CD1 C N N 186 LEU CD2 C N N 187 LEU OXT O N N 188 LEU H H N N 189 LEU H2 H N N 190 LEU HA H N N 191 LEU HB2 H N N 192 LEU HB3 H N N 193 LEU HG H N N 194 LEU HD11 H N N 195 LEU HD12 H N N 196 LEU HD13 H N N 197 LEU HD21 H N N 198 LEU HD22 H N N 199 LEU HD23 H N N 200 LEU HXT H N N 201 LYS N N N N 202 LYS CA C N S 203 LYS C C N N 204 LYS O O N N 205 LYS CB C N N 206 LYS CG C N N 207 LYS CD C N N 208 LYS CE C N N 209 LYS NZ N N N 210 LYS OXT O N N 211 LYS H H N N 212 LYS H2 H N N 213 LYS HA H N N 214 LYS HB2 H N N 215 LYS HB3 H N N 216 LYS HG2 H N N 217 LYS HG3 H N N 218 LYS HD2 H N N 219 LYS HD3 H N N 220 LYS HE2 H N N 221 LYS HE3 H N N 222 LYS HZ1 H N N 223 LYS HZ2 H N N 224 LYS HZ3 H N N 225 LYS HXT H N N 226 MET N N N N 227 MET CA C N S 228 MET C C N N 229 MET O O N N 230 MET CB C N N 231 MET CG C N N 232 MET SD S N N 233 MET CE C N N 234 MET OXT O N N 235 MET H H N N 236 MET H2 H N N 237 MET HA H N N 238 MET HB2 H N N 239 MET HB3 H N N 240 MET HG2 H N N 241 MET HG3 H N N 242 MET HE1 H N N 243 MET HE2 H N N 244 MET HE3 H N N 245 MET HXT H N N 246 PHE N N N N 247 PHE CA C N S 248 PHE C C N N 249 PHE O O N N 250 PHE CB C N N 251 PHE CG C Y N 252 PHE CD1 C Y N 253 PHE CD2 C Y N 254 PHE CE1 C Y N 255 PHE CE2 C Y N 256 PHE CZ C Y N 257 PHE OXT O N N 258 PHE H H N N 259 PHE H2 H N N 260 PHE HA H N N 261 PHE HB2 H N N 262 PHE HB3 H N N 263 PHE HD1 H N N 264 PHE HD2 H N N 265 PHE HE1 H N N 266 PHE HE2 H N N 267 PHE HZ H N N 268 PHE HXT H N N 269 PRO N N N N 270 PRO CA C N S 271 PRO C C N N 272 PRO O O N N 273 PRO CB C N N 274 PRO CG C N N 275 PRO CD C N N 276 PRO OXT O N N 277 PRO H H N N 278 PRO HA H N N 279 PRO HB2 H N N 280 PRO HB3 H N N 281 PRO HG2 H N N 282 PRO HG3 H N N 283 PRO HD2 H N N 284 PRO HD3 H N N 285 PRO HXT H N N 286 SER N N N N 287 SER CA C N S 288 SER C C N N 289 SER O O N N 290 SER CB C N N 291 SER OG O N N 292 SER OXT O N N 293 SER H H N N 294 SER H2 H N N 295 SER HA H N N 296 SER HB2 H N N 297 SER HB3 H N N 298 SER HG H N N 299 SER HXT H N N 300 THR N N N N 301 THR CA C N S 302 THR C C N N 303 THR O O N N 304 THR CB C N R 305 THR OG1 O N N 306 THR CG2 C N N 307 THR OXT O N N 308 THR H H N N 309 THR H2 H N N 310 THR HA H N N 311 THR HB H N N 312 THR HG1 H N N 313 THR HG21 H N N 314 THR HG22 H N N 315 THR HG23 H N N 316 THR HXT H N N 317 TRP N N N N 318 TRP CA C N S 319 TRP C C N N 320 TRP O O N N 321 TRP CB C N N 322 TRP CG C Y N 323 TRP CD1 C Y N 324 TRP CD2 C Y N 325 TRP NE1 N Y N 326 TRP CE2 C Y N 327 TRP CE3 C Y N 328 TRP CZ2 C Y N 329 TRP CZ3 C Y N 330 TRP CH2 C Y N 331 TRP OXT O N N 332 TRP H H N N 333 TRP H2 H N N 334 TRP HA H N N 335 TRP HB2 H N N 336 TRP HB3 H N N 337 TRP HD1 H N N 338 TRP HE1 H N N 339 TRP HE3 H N N 340 TRP HZ2 H N N 341 TRP HZ3 H N N 342 TRP HH2 H N N 343 TRP HXT H N N 344 TYR N N N N 345 TYR CA C N S 346 TYR C C N N 347 TYR O O N N 348 TYR CB C N N 349 TYR CG C Y N 350 TYR CD1 C Y N 351 TYR CD2 C Y N 352 TYR CE1 C Y N 353 TYR CE2 C Y N 354 TYR CZ C Y N 355 TYR OH O N N 356 TYR OXT O N N 357 TYR H H N N 358 TYR H2 H N N 359 TYR HA H N N 360 TYR HB2 H N N 361 TYR HB3 H N N 362 TYR HD1 H N N 363 TYR HD2 H N N 364 TYR HE1 H N N 365 TYR HE2 H N N 366 TYR HH H N N 367 TYR HXT H N N 368 VAL N N N N 369 VAL CA C N S 370 VAL C C N N 371 VAL O O N N 372 VAL CB C N N 373 VAL CG1 C N N 374 VAL CG2 C N N 375 VAL OXT O N N 376 VAL H H N N 377 VAL H2 H N N 378 VAL HA H N N 379 VAL HB H N N 380 VAL HG11 H N N 381 VAL HG12 H N N 382 VAL HG13 H N N 383 VAL HG21 H N N 384 VAL HG22 H N N 385 VAL HG23 H N N 386 VAL HXT H N N 387 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 CYS N CA sing N N 70 CYS N H sing N N 71 CYS N H2 sing N N 72 CYS CA C sing N N 73 CYS CA CB sing N N 74 CYS CA HA sing N N 75 CYS C O doub N N 76 CYS C OXT sing N N 77 CYS CB SG sing N N 78 CYS CB HB2 sing N N 79 CYS CB HB3 sing N N 80 CYS SG HG sing N N 81 CYS OXT HXT sing N N 82 GLN N CA sing N N 83 GLN N H sing N N 84 GLN N H2 sing N N 85 GLN CA C sing N N 86 GLN CA CB sing N N 87 GLN CA HA sing N N 88 GLN C O doub N N 89 GLN C OXT sing N N 90 GLN CB CG sing N N 91 GLN CB HB2 sing N N 92 GLN CB HB3 sing N N 93 GLN CG CD sing N N 94 GLN CG HG2 sing N N 95 GLN CG HG3 sing N N 96 GLN CD OE1 doub N N 97 GLN CD NE2 sing N N 98 GLN NE2 HE21 sing N N 99 GLN NE2 HE22 sing N N 100 GLN OXT HXT sing N N 101 GLU N CA sing N N 102 GLU N H sing N N 103 GLU N H2 sing N N 104 GLU CA C sing N N 105 GLU CA CB sing N N 106 GLU CA HA sing N N 107 GLU C O doub N N 108 GLU C OXT sing N N 109 GLU CB CG sing N N 110 GLU CB HB2 sing N N 111 GLU CB HB3 sing N N 112 GLU CG CD sing N N 113 GLU CG HG2 sing N N 114 GLU CG HG3 sing N N 115 GLU CD OE1 doub N N 116 GLU CD OE2 sing N N 117 GLU OE2 HE2 sing N N 118 GLU OXT HXT sing N N 119 GLY N CA sing N N 120 GLY N H sing N N 121 GLY N H2 sing N N 122 GLY CA C sing N N 123 GLY CA HA2 sing N N 124 GLY CA HA3 sing N N 125 GLY C O doub N N 126 GLY C OXT sing N N 127 GLY OXT HXT sing N N 128 HIS N CA sing N N 129 HIS N H sing N N 130 HIS N H2 sing N N 131 HIS CA C sing N N 132 HIS CA CB sing N N 133 HIS CA HA sing N N 134 HIS C O doub N N 135 HIS C OXT sing N N 136 HIS CB CG sing N N 137 HIS CB HB2 sing N N 138 HIS CB HB3 sing N N 139 HIS CG ND1 sing Y N 140 HIS CG CD2 doub Y N 141 HIS ND1 CE1 doub Y N 142 HIS ND1 HD1 sing N N 143 HIS CD2 NE2 sing Y N 144 HIS CD2 HD2 sing N N 145 HIS CE1 NE2 sing Y N 146 HIS CE1 HE1 sing N N 147 HIS NE2 HE2 sing N N 148 HIS OXT HXT sing N N 149 ILE N CA sing N N 150 ILE N H sing N N 151 ILE N H2 sing N N 152 ILE CA C sing N N 153 ILE CA CB sing N N 154 ILE CA HA sing N N 155 ILE C O doub N N 156 ILE C OXT sing N N 157 ILE CB CG1 sing N N 158 ILE CB CG2 sing N N 159 ILE CB HB sing N N 160 ILE CG1 CD1 sing N N 161 ILE CG1 HG12 sing N N 162 ILE CG1 HG13 sing N N 163 ILE CG2 HG21 sing N N 164 ILE CG2 HG22 sing N N 165 ILE CG2 HG23 sing N N 166 ILE CD1 HD11 sing N N 167 ILE CD1 HD12 sing N N 168 ILE CD1 HD13 sing N N 169 ILE OXT HXT sing N N 170 LEU N CA sing N N 171 LEU N H sing N N 172 LEU N H2 sing N N 173 LEU CA C sing N N 174 LEU CA CB sing N N 175 LEU CA HA sing N N 176 LEU C O doub N N 177 LEU C OXT sing N N 178 LEU CB CG sing N N 179 LEU CB HB2 sing N N 180 LEU CB HB3 sing N N 181 LEU CG CD1 sing N N 182 LEU CG CD2 sing N N 183 LEU CG HG sing N N 184 LEU CD1 HD11 sing N N 185 LEU CD1 HD12 sing N N 186 LEU CD1 HD13 sing N N 187 LEU CD2 HD21 sing N N 188 LEU CD2 HD22 sing N N 189 LEU CD2 HD23 sing N N 190 LEU OXT HXT sing N N 191 LYS N CA sing N N 192 LYS N H sing N N 193 LYS N H2 sing N N 194 LYS CA C sing N N 195 LYS CA CB sing N N 196 LYS CA HA sing N N 197 LYS C O doub N N 198 LYS C OXT sing N N 199 LYS CB CG sing N N 200 LYS CB HB2 sing N N 201 LYS CB HB3 sing N N 202 LYS CG CD sing N N 203 LYS CG HG2 sing N N 204 LYS CG HG3 sing N N 205 LYS CD CE sing N N 206 LYS CD HD2 sing N N 207 LYS CD HD3 sing N N 208 LYS CE NZ sing N N 209 LYS CE HE2 sing N N 210 LYS CE HE3 sing N N 211 LYS NZ HZ1 sing N N 212 LYS NZ HZ2 sing N N 213 LYS NZ HZ3 sing N N 214 LYS OXT HXT sing N N 215 MET N CA sing N N 216 MET N H sing N N 217 MET N H2 sing N N 218 MET CA C sing N N 219 MET CA CB sing N N 220 MET CA HA sing N N 221 MET C O doub N N 222 MET C OXT sing N N 223 MET CB CG sing N N 224 MET CB HB2 sing N N 225 MET CB HB3 sing N N 226 MET CG SD sing N N 227 MET CG HG2 sing N N 228 MET CG HG3 sing N N 229 MET SD CE sing N N 230 MET CE HE1 sing N N 231 MET CE HE2 sing N N 232 MET CE HE3 sing N N 233 MET OXT HXT sing N N 234 PHE N CA sing N N 235 PHE N H sing N N 236 PHE N H2 sing N N 237 PHE CA C sing N N 238 PHE CA CB sing N N 239 PHE CA HA sing N N 240 PHE C O doub N N 241 PHE C OXT sing N N 242 PHE CB CG sing N N 243 PHE CB HB2 sing N N 244 PHE CB HB3 sing N N 245 PHE CG CD1 doub Y N 246 PHE CG CD2 sing Y N 247 PHE CD1 CE1 sing Y N 248 PHE CD1 HD1 sing N N 249 PHE CD2 CE2 doub Y N 250 PHE CD2 HD2 sing N N 251 PHE CE1 CZ doub Y N 252 PHE CE1 HE1 sing N N 253 PHE CE2 CZ sing Y N 254 PHE CE2 HE2 sing N N 255 PHE CZ HZ sing N N 256 PHE OXT HXT sing N N 257 PRO N CA sing N N 258 PRO N CD sing N N 259 PRO N H sing N N 260 PRO CA C sing N N 261 PRO CA CB sing N N 262 PRO CA HA sing N N 263 PRO C O doub N N 264 PRO C OXT sing N N 265 PRO CB CG sing N N 266 PRO CB HB2 sing N N 267 PRO CB HB3 sing N N 268 PRO CG CD sing N N 269 PRO CG HG2 sing N N 270 PRO CG HG3 sing N N 271 PRO CD HD2 sing N N 272 PRO CD HD3 sing N N 273 PRO OXT HXT sing N N 274 SER N CA sing N N 275 SER N H sing N N 276 SER N H2 sing N N 277 SER CA C sing N N 278 SER CA CB sing N N 279 SER CA HA sing N N 280 SER C O doub N N 281 SER C OXT sing N N 282 SER CB OG sing N N 283 SER CB HB2 sing N N 284 SER CB HB3 sing N N 285 SER OG HG sing N N 286 SER OXT HXT sing N N 287 THR N CA sing N N 288 THR N H sing N N 289 THR N H2 sing N N 290 THR CA C sing N N 291 THR CA CB sing N N 292 THR CA HA sing N N 293 THR C O doub N N 294 THR C OXT sing N N 295 THR CB OG1 sing N N 296 THR CB CG2 sing N N 297 THR CB HB sing N N 298 THR OG1 HG1 sing N N 299 THR CG2 HG21 sing N N 300 THR CG2 HG22 sing N N 301 THR CG2 HG23 sing N N 302 THR OXT HXT sing N N 303 TRP N CA sing N N 304 TRP N H sing N N 305 TRP N H2 sing N N 306 TRP CA C sing N N 307 TRP CA CB sing N N 308 TRP CA HA sing N N 309 TRP C O doub N N 310 TRP C OXT sing N N 311 TRP CB CG sing N N 312 TRP CB HB2 sing N N 313 TRP CB HB3 sing N N 314 TRP CG CD1 doub Y N 315 TRP CG CD2 sing Y N 316 TRP CD1 NE1 sing Y N 317 TRP CD1 HD1 sing N N 318 TRP CD2 CE2 doub Y N 319 TRP CD2 CE3 sing Y N 320 TRP NE1 CE2 sing Y N 321 TRP NE1 HE1 sing N N 322 TRP CE2 CZ2 sing Y N 323 TRP CE3 CZ3 doub Y N 324 TRP CE3 HE3 sing N N 325 TRP CZ2 CH2 doub Y N 326 TRP CZ2 HZ2 sing N N 327 TRP CZ3 CH2 sing Y N 328 TRP CZ3 HZ3 sing N N 329 TRP CH2 HH2 sing N N 330 TRP OXT HXT sing N N 331 TYR N CA sing N N 332 TYR N H sing N N 333 TYR N H2 sing N N 334 TYR CA C sing N N 335 TYR CA CB sing N N 336 TYR CA HA sing N N 337 TYR C O doub N N 338 TYR C OXT sing N N 339 TYR CB CG sing N N 340 TYR CB HB2 sing N N 341 TYR CB HB3 sing N N 342 TYR CG CD1 doub Y N 343 TYR CG CD2 sing Y N 344 TYR CD1 CE1 sing Y N 345 TYR CD1 HD1 sing N N 346 TYR CD2 CE2 doub Y N 347 TYR CD2 HD2 sing N N 348 TYR CE1 CZ doub Y N 349 TYR CE1 HE1 sing N N 350 TYR CE2 CZ sing Y N 351 TYR CE2 HE2 sing N N 352 TYR CZ OH sing N N 353 TYR OH HH sing N N 354 TYR OXT HXT sing N N 355 VAL N CA sing N N 356 VAL N H sing N N 357 VAL N H2 sing N N 358 VAL CA C sing N N 359 VAL CA CB sing N N 360 VAL CA HA sing N N 361 VAL C O doub N N 362 VAL C OXT sing N N 363 VAL CB CG1 sing N N 364 VAL CB CG2 sing N N 365 VAL CB HB sing N N 366 VAL CG1 HG11 sing N N 367 VAL CG1 HG12 sing N N 368 VAL CG1 HG13 sing N N 369 VAL CG2 HG21 sing N N 370 VAL CG2 HG22 sing N N 371 VAL CG2 HG23 sing N N 372 VAL OXT HXT sing N N 373 # _em_admin.current_status REL _em_admin.deposition_date 2024-02-06 _em_admin.deposition_site PDBJ _em_admin.entry_id 8Y8X _em_admin.last_update 2025-07-02 _em_admin.map_release_date 2025-03-19 _em_admin.title 'Cryo-EM structure of GlpF with P177 deletion in POPC nanodisc' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 562 _em_entity_assembly_naturalsource.organism 'Escherichia coli' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 7108 _em_entity_assembly_recombinant.organism 'Spodoptera frugiperda' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 63.4 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K2 SUMMIT (4k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? ? ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? ? ? ? ? 'MODEL REFINEMENT' ? 8 ? ? ? PHENIX ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science (JSPS)' Japan 20H00451 1 'Japan Agency for Medical Research and Development (AMED)' Japan JP21ae0121028 2 # _atom_sites.entry_id 8Y8X _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_ #