data_9JST # _entry.id 9JST # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.397 _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 9JST pdb_00009jst 10.2210/pdb9jst/pdb WWPDB D_1300052118 ? ? EMDB EMD-61782 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2024-10-09 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9JST _pdbx_database_status.recvd_initial_deposition_date 2024-10-01 _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 'Wild-type native PMEL amyloid - polymorph 1' _pdbx_database_related.db_id EMD-61782 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email toda@yamanashi.ac.jp _pdbx_contact_author.name_first Toshiyuki _pdbx_contact_author.name_last Oda _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-8090-2159 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Oda, T.' 1 0000-0001-8090-2159 'Yanagisawa, H.' 2 0000-0003-0313-2343 # _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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Cryo-EM of PMEL Amyloids Reveals Pathogenic Mechanism of G175S in Pigment Dispersion Syndrome.' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yanagisawa, H.' 1 0000-0003-0313-2343 primary 'Oda, T.' 2 0000-0001-8090-2159 # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description M-alpha _entity.formula_weight 3843.394 _entity.pdbx_number_of_molecules 8 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name '95 kDa melanocyte-specific secreted glycoprotein,P26,Secreted melanoma-associated ME20 antigen,ME20-S,ME20S' # _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 SFVYVWKTWGQYWQVLGGPVSGLSIGTGRAMLGTH _entity_poly.pdbx_seq_one_letter_code_can SFVYVWKTWGQYWQVLGGPVSGLSIGTGRAMLGTH _entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H _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 SER n 1 2 PHE n 1 3 VAL n 1 4 TYR n 1 5 VAL n 1 6 TRP n 1 7 LYS n 1 8 THR n 1 9 TRP n 1 10 GLY n 1 11 GLN n 1 12 TYR n 1 13 TRP n 1 14 GLN n 1 15 VAL n 1 16 LEU n 1 17 GLY n 1 18 GLY n 1 19 PRO n 1 20 VAL n 1 21 SER n 1 22 GLY n 1 23 LEU n 1 24 SER n 1 25 ILE n 1 26 GLY n 1 27 THR n 1 28 GLY n 1 29 ARG n 1 30 ALA n 1 31 MET n 1 32 LEU n 1 33 GLY n 1 34 THR n 1 35 HIS n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 35 _entity_src_nat.common_name human _entity_src_nat.pdbx_organism_scientific 'Homo sapiens' _entity_src_nat.pdbx_ncbi_taxonomy_id 9606 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue 'Vagina melanoma' _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line HMV-II _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 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 SER 1 148 148 SER SER A . n A 1 2 PHE 2 149 149 PHE PHE A . n A 1 3 VAL 3 150 150 VAL VAL A . n A 1 4 TYR 4 151 151 TYR TYR A . n A 1 5 VAL 5 152 152 VAL VAL A . n A 1 6 TRP 6 153 153 TRP TRP A . n A 1 7 LYS 7 154 154 LYS LYS A . n A 1 8 THR 8 155 155 THR THR A . n A 1 9 TRP 9 156 156 TRP TRP A . n A 1 10 GLY 10 157 157 GLY GLY A . n A 1 11 GLN 11 158 158 GLN GLN A . n A 1 12 TYR 12 159 159 TYR TYR A . n A 1 13 TRP 13 160 160 TRP TRP A . n A 1 14 GLN 14 161 161 GLN GLN A . n A 1 15 VAL 15 162 162 VAL VAL A . n A 1 16 LEU 16 163 163 LEU LEU A . n A 1 17 GLY 17 164 164 GLY GLY A . n A 1 18 GLY 18 165 165 GLY GLY A . n A 1 19 PRO 19 166 166 PRO PRO A . n A 1 20 VAL 20 167 167 VAL VAL A . n A 1 21 SER 21 168 168 SER SER A . n A 1 22 GLY 22 169 169 GLY GLY A . n A 1 23 LEU 23 170 170 LEU LEU A . n A 1 24 SER 24 171 171 SER SER A . n A 1 25 ILE 25 172 172 ILE ILE A . n A 1 26 GLY 26 173 173 GLY GLY A . n A 1 27 THR 27 174 174 THR THR A . n A 1 28 GLY 28 175 175 GLY GLY A . n A 1 29 ARG 29 176 176 ARG ARG A . n A 1 30 ALA 30 177 177 ALA ALA A . n A 1 31 MET 31 178 178 MET MET A . n A 1 32 LEU 32 179 179 LEU LEU A . n A 1 33 GLY 33 180 180 GLY GLY A . n A 1 34 THR 34 181 181 THR THR A . n A 1 35 HIS 35 182 182 HIS HIS A . n B 1 1 SER 1 148 148 SER SER B . n B 1 2 PHE 2 149 149 PHE PHE B . n B 1 3 VAL 3 150 150 VAL VAL B . n B 1 4 TYR 4 151 151 TYR TYR B . n B 1 5 VAL 5 152 152 VAL VAL B . n B 1 6 TRP 6 153 153 TRP TRP B . n B 1 7 LYS 7 154 154 LYS LYS B . n B 1 8 THR 8 155 155 THR THR B . n B 1 9 TRP 9 156 156 TRP TRP B . n B 1 10 GLY 10 157 157 GLY GLY B . n B 1 11 GLN 11 158 158 GLN GLN B . n B 1 12 TYR 12 159 159 TYR TYR B . n B 1 13 TRP 13 160 160 TRP TRP B . n B 1 14 GLN 14 161 161 GLN GLN B . n B 1 15 VAL 15 162 162 VAL VAL B . n B 1 16 LEU 16 163 163 LEU LEU B . n B 1 17 GLY 17 164 164 GLY GLY B . n B 1 18 GLY 18 165 165 GLY GLY B . n B 1 19 PRO 19 166 166 PRO PRO B . n B 1 20 VAL 20 167 167 VAL VAL B . n B 1 21 SER 21 168 168 SER SER B . n B 1 22 GLY 22 169 169 GLY GLY B . n B 1 23 LEU 23 170 170 LEU LEU B . n B 1 24 SER 24 171 171 SER SER B . n B 1 25 ILE 25 172 172 ILE ILE B . n B 1 26 GLY 26 173 173 GLY GLY B . n B 1 27 THR 27 174 174 THR THR B . n B 1 28 GLY 28 175 175 GLY GLY B . n B 1 29 ARG 29 176 176 ARG ARG B . n B 1 30 ALA 30 177 177 ALA ALA B . n B 1 31 MET 31 178 178 MET MET B . n B 1 32 LEU 32 179 179 LEU LEU B . n B 1 33 GLY 33 180 180 GLY GLY B . n B 1 34 THR 34 181 181 THR THR B . n B 1 35 HIS 35 182 182 HIS HIS B . n C 1 1 SER 1 148 148 SER SER C . n C 1 2 PHE 2 149 149 PHE PHE C . n C 1 3 VAL 3 150 150 VAL VAL C . n C 1 4 TYR 4 151 151 TYR TYR C . n C 1 5 VAL 5 152 152 VAL VAL C . n C 1 6 TRP 6 153 153 TRP TRP C . n C 1 7 LYS 7 154 154 LYS LYS C . n C 1 8 THR 8 155 155 THR THR C . n C 1 9 TRP 9 156 156 TRP TRP C . n C 1 10 GLY 10 157 157 GLY GLY C . n C 1 11 GLN 11 158 158 GLN GLN C . n C 1 12 TYR 12 159 159 TYR TYR C . n C 1 13 TRP 13 160 160 TRP TRP C . n C 1 14 GLN 14 161 161 GLN GLN C . n C 1 15 VAL 15 162 162 VAL VAL C . n C 1 16 LEU 16 163 163 LEU LEU C . n C 1 17 GLY 17 164 164 GLY GLY C . n C 1 18 GLY 18 165 165 GLY GLY C . n C 1 19 PRO 19 166 166 PRO PRO C . n C 1 20 VAL 20 167 167 VAL VAL C . n C 1 21 SER 21 168 168 SER SER C . n C 1 22 GLY 22 169 169 GLY GLY C . n C 1 23 LEU 23 170 170 LEU LEU C . n C 1 24 SER 24 171 171 SER SER C . n C 1 25 ILE 25 172 172 ILE ILE C . n C 1 26 GLY 26 173 173 GLY GLY C . n C 1 27 THR 27 174 174 THR THR C . n C 1 28 GLY 28 175 175 GLY GLY C . n C 1 29 ARG 29 176 176 ARG ARG C . n C 1 30 ALA 30 177 177 ALA ALA C . n C 1 31 MET 31 178 178 MET MET C . n C 1 32 LEU 32 179 179 LEU LEU C . n C 1 33 GLY 33 180 180 GLY GLY C . n C 1 34 THR 34 181 181 THR THR C . n C 1 35 HIS 35 182 182 HIS HIS C . n D 1 1 SER 1 148 148 SER SER D . n D 1 2 PHE 2 149 149 PHE PHE D . n D 1 3 VAL 3 150 150 VAL VAL D . n D 1 4 TYR 4 151 151 TYR TYR D . n D 1 5 VAL 5 152 152 VAL VAL D . n D 1 6 TRP 6 153 153 TRP TRP D . n D 1 7 LYS 7 154 154 LYS LYS D . n D 1 8 THR 8 155 155 THR THR D . n D 1 9 TRP 9 156 156 TRP TRP D . n D 1 10 GLY 10 157 157 GLY GLY D . n D 1 11 GLN 11 158 158 GLN GLN D . n D 1 12 TYR 12 159 159 TYR TYR D . n D 1 13 TRP 13 160 160 TRP TRP D . n D 1 14 GLN 14 161 161 GLN GLN D . n D 1 15 VAL 15 162 162 VAL VAL D . n D 1 16 LEU 16 163 163 LEU LEU D . n D 1 17 GLY 17 164 164 GLY GLY D . n D 1 18 GLY 18 165 165 GLY GLY D . n D 1 19 PRO 19 166 166 PRO PRO D . n D 1 20 VAL 20 167 167 VAL VAL D . n D 1 21 SER 21 168 168 SER SER D . n D 1 22 GLY 22 169 169 GLY GLY D . n D 1 23 LEU 23 170 170 LEU LEU D . n D 1 24 SER 24 171 171 SER SER D . n D 1 25 ILE 25 172 172 ILE ILE D . n D 1 26 GLY 26 173 173 GLY GLY D . n D 1 27 THR 27 174 174 THR THR D . n D 1 28 GLY 28 175 175 GLY GLY D . n D 1 29 ARG 29 176 176 ARG ARG D . n D 1 30 ALA 30 177 177 ALA ALA D . n D 1 31 MET 31 178 178 MET MET D . n D 1 32 LEU 32 179 179 LEU LEU D . n D 1 33 GLY 33 180 180 GLY GLY D . n D 1 34 THR 34 181 181 THR THR D . n D 1 35 HIS 35 182 182 HIS HIS D . n E 1 1 SER 1 148 148 SER SER E . n E 1 2 PHE 2 149 149 PHE PHE E . n E 1 3 VAL 3 150 150 VAL VAL E . n E 1 4 TYR 4 151 151 TYR TYR E . n E 1 5 VAL 5 152 152 VAL VAL E . n E 1 6 TRP 6 153 153 TRP TRP E . n E 1 7 LYS 7 154 154 LYS LYS E . n E 1 8 THR 8 155 155 THR THR E . n E 1 9 TRP 9 156 156 TRP TRP E . n E 1 10 GLY 10 157 157 GLY GLY E . n E 1 11 GLN 11 158 158 GLN GLN E . n E 1 12 TYR 12 159 159 TYR TYR E . n E 1 13 TRP 13 160 160 TRP TRP E . n E 1 14 GLN 14 161 161 GLN GLN E . n E 1 15 VAL 15 162 162 VAL VAL E . n E 1 16 LEU 16 163 163 LEU LEU E . n E 1 17 GLY 17 164 164 GLY GLY E . n E 1 18 GLY 18 165 165 GLY GLY E . n E 1 19 PRO 19 166 166 PRO PRO E . n E 1 20 VAL 20 167 167 VAL VAL E . n E 1 21 SER 21 168 168 SER SER E . n E 1 22 GLY 22 169 169 GLY GLY E . n E 1 23 LEU 23 170 170 LEU LEU E . n E 1 24 SER 24 171 171 SER SER E . n E 1 25 ILE 25 172 172 ILE ILE E . n E 1 26 GLY 26 173 173 GLY GLY E . n E 1 27 THR 27 174 174 THR THR E . n E 1 28 GLY 28 175 175 GLY GLY E . n E 1 29 ARG 29 176 176 ARG ARG E . n E 1 30 ALA 30 177 177 ALA ALA E . n E 1 31 MET 31 178 178 MET MET E . n E 1 32 LEU 32 179 179 LEU LEU E . n E 1 33 GLY 33 180 180 GLY GLY E . n E 1 34 THR 34 181 181 THR THR E . n E 1 35 HIS 35 182 182 HIS HIS E . n F 1 1 SER 1 148 148 SER SER F . n F 1 2 PHE 2 149 149 PHE PHE F . n F 1 3 VAL 3 150 150 VAL VAL F . n F 1 4 TYR 4 151 151 TYR TYR F . n F 1 5 VAL 5 152 152 VAL VAL F . n F 1 6 TRP 6 153 153 TRP TRP F . n F 1 7 LYS 7 154 154 LYS LYS F . n F 1 8 THR 8 155 155 THR THR F . n F 1 9 TRP 9 156 156 TRP TRP F . n F 1 10 GLY 10 157 157 GLY GLY F . n F 1 11 GLN 11 158 158 GLN GLN F . n F 1 12 TYR 12 159 159 TYR TYR F . n F 1 13 TRP 13 160 160 TRP TRP F . n F 1 14 GLN 14 161 161 GLN GLN F . n F 1 15 VAL 15 162 162 VAL VAL F . n F 1 16 LEU 16 163 163 LEU LEU F . n F 1 17 GLY 17 164 164 GLY GLY F . n F 1 18 GLY 18 165 165 GLY GLY F . n F 1 19 PRO 19 166 166 PRO PRO F . n F 1 20 VAL 20 167 167 VAL VAL F . n F 1 21 SER 21 168 168 SER SER F . n F 1 22 GLY 22 169 169 GLY GLY F . n F 1 23 LEU 23 170 170 LEU LEU F . n F 1 24 SER 24 171 171 SER SER F . n F 1 25 ILE 25 172 172 ILE ILE F . n F 1 26 GLY 26 173 173 GLY GLY F . n F 1 27 THR 27 174 174 THR THR F . n F 1 28 GLY 28 175 175 GLY GLY F . n F 1 29 ARG 29 176 176 ARG ARG F . n F 1 30 ALA 30 177 177 ALA ALA F . n F 1 31 MET 31 178 178 MET MET F . n F 1 32 LEU 32 179 179 LEU LEU F . n F 1 33 GLY 33 180 180 GLY GLY F . n F 1 34 THR 34 181 181 THR THR F . n F 1 35 HIS 35 182 182 HIS HIS F . n G 1 1 SER 1 148 148 SER SER G . n G 1 2 PHE 2 149 149 PHE PHE G . n G 1 3 VAL 3 150 150 VAL VAL G . n G 1 4 TYR 4 151 151 TYR TYR G . n G 1 5 VAL 5 152 152 VAL VAL G . n G 1 6 TRP 6 153 153 TRP TRP G . n G 1 7 LYS 7 154 154 LYS LYS G . n G 1 8 THR 8 155 155 THR THR G . n G 1 9 TRP 9 156 156 TRP TRP G . n G 1 10 GLY 10 157 157 GLY GLY G . n G 1 11 GLN 11 158 158 GLN GLN G . n G 1 12 TYR 12 159 159 TYR TYR G . n G 1 13 TRP 13 160 160 TRP TRP G . n G 1 14 GLN 14 161 161 GLN GLN G . n G 1 15 VAL 15 162 162 VAL VAL G . n G 1 16 LEU 16 163 163 LEU LEU G . n G 1 17 GLY 17 164 164 GLY GLY G . n G 1 18 GLY 18 165 165 GLY GLY G . n G 1 19 PRO 19 166 166 PRO PRO G . n G 1 20 VAL 20 167 167 VAL VAL G . n G 1 21 SER 21 168 168 SER SER G . n G 1 22 GLY 22 169 169 GLY GLY G . n G 1 23 LEU 23 170 170 LEU LEU G . n G 1 24 SER 24 171 171 SER SER G . n G 1 25 ILE 25 172 172 ILE ILE G . n G 1 26 GLY 26 173 173 GLY GLY G . n G 1 27 THR 27 174 174 THR THR G . n G 1 28 GLY 28 175 175 GLY GLY G . n G 1 29 ARG 29 176 176 ARG ARG G . n G 1 30 ALA 30 177 177 ALA ALA G . n G 1 31 MET 31 178 178 MET MET G . n G 1 32 LEU 32 179 179 LEU LEU G . n G 1 33 GLY 33 180 180 GLY GLY G . n G 1 34 THR 34 181 181 THR THR G . n G 1 35 HIS 35 182 182 HIS HIS G . n H 1 1 SER 1 148 148 SER SER H . n H 1 2 PHE 2 149 149 PHE PHE H . n H 1 3 VAL 3 150 150 VAL VAL H . n H 1 4 TYR 4 151 151 TYR TYR H . n H 1 5 VAL 5 152 152 VAL VAL H . n H 1 6 TRP 6 153 153 TRP TRP H . n H 1 7 LYS 7 154 154 LYS LYS H . n H 1 8 THR 8 155 155 THR THR H . n H 1 9 TRP 9 156 156 TRP TRP H . n H 1 10 GLY 10 157 157 GLY GLY H . n H 1 11 GLN 11 158 158 GLN GLN H . n H 1 12 TYR 12 159 159 TYR TYR H . n H 1 13 TRP 13 160 160 TRP TRP H . n H 1 14 GLN 14 161 161 GLN GLN H . n H 1 15 VAL 15 162 162 VAL VAL H . n H 1 16 LEU 16 163 163 LEU LEU H . n H 1 17 GLY 17 164 164 GLY GLY H . n H 1 18 GLY 18 165 165 GLY GLY H . n H 1 19 PRO 19 166 166 PRO PRO H . n H 1 20 VAL 20 167 167 VAL VAL H . n H 1 21 SER 21 168 168 SER SER H . n H 1 22 GLY 22 169 169 GLY GLY H . n H 1 23 LEU 23 170 170 LEU LEU H . n H 1 24 SER 24 171 171 SER SER H . n H 1 25 ILE 25 172 172 ILE ILE H . n H 1 26 GLY 26 173 173 GLY GLY H . n H 1 27 THR 27 174 174 THR THR H . n H 1 28 GLY 28 175 175 GLY GLY H . n H 1 29 ARG 29 176 176 ARG ARG H . n H 1 30 ALA 30 177 177 ALA ALA H . n H 1 31 MET 31 178 178 MET MET H . n H 1 32 LEU 32 179 179 LEU LEU H . n H 1 33 GLY 33 180 180 GLY GLY H . n H 1 34 THR 34 181 181 THR THR H . n H 1 35 HIS 35 182 182 HIS HIS H . 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 9JST _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 9JST _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 9JST _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 9JST _struct.title 'Wild-type native PMEL amyloid - polymorph 1' _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 9JST _struct_keywords.text 'melanosome, melanoma, pigment, melanin, amyloid, glaucoma, STRUCTURAL PROTEIN' _struct_keywords.pdbx_keywords 'STRUCTURAL PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 1 ? F N N 1 ? G N N 1 ? H N N 1 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PMEL_HUMAN _struct_ref.pdbx_db_accession P40967 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code SFVYVWKTWGQYWQVLGGPVSGLSIGTGRAMLGTH _struct_ref.pdbx_align_begin 148 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 9JST A 1 ? 35 ? P40967 148 ? 182 ? 148 182 2 1 9JST B 1 ? 35 ? P40967 148 ? 182 ? 148 182 3 1 9JST C 1 ? 35 ? P40967 148 ? 182 ? 148 182 4 1 9JST D 1 ? 35 ? P40967 148 ? 182 ? 148 182 5 1 9JST E 1 ? 35 ? P40967 148 ? 182 ? 148 182 6 1 9JST F 1 ? 35 ? P40967 148 ? 182 ? 148 182 7 1 9JST G 1 ? 35 ? P40967 148 ? 182 ? 148 182 8 1 9JST H 1 ? 35 ? P40967 148 ? 182 ? 148 182 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _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' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 4 ? AA3 ? 4 ? AA4 ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? parallel AA1 2 3 ? parallel AA1 3 4 ? parallel AA2 1 2 ? parallel AA2 2 3 ? parallel AA2 3 4 ? parallel AA3 1 2 ? parallel AA3 2 3 ? parallel AA3 3 4 ? parallel AA4 1 2 ? parallel AA4 2 3 ? parallel AA4 3 4 ? parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 PHE A 2 ? GLY A 17 ? PHE A 149 GLY A 164 AA1 2 PHE B 2 ? GLY B 17 ? PHE B 149 GLY B 164 AA1 3 PHE C 2 ? GLY C 17 ? PHE C 149 GLY C 164 AA1 4 PHE D 2 ? GLY D 17 ? PHE D 149 GLY D 164 AA2 1 VAL A 20 ? LEU A 32 ? VAL A 167 LEU A 179 AA2 2 VAL B 20 ? LEU B 32 ? VAL B 167 LEU B 179 AA2 3 VAL C 20 ? LEU C 32 ? VAL C 167 LEU C 179 AA2 4 VAL D 20 ? LEU D 32 ? VAL D 167 LEU D 179 AA3 1 PHE E 2 ? GLY E 17 ? PHE E 149 GLY E 164 AA3 2 PHE F 2 ? GLY F 17 ? PHE F 149 GLY F 164 AA3 3 PHE G 2 ? GLY G 17 ? PHE G 149 GLY G 164 AA3 4 PHE H 2 ? GLY H 17 ? PHE H 149 GLY H 164 AA4 1 VAL E 20 ? LEU E 32 ? VAL E 167 LEU E 179 AA4 2 VAL F 20 ? LEU F 32 ? VAL F 167 LEU F 179 AA4 3 VAL G 20 ? LEU G 32 ? VAL G 167 LEU G 179 AA4 4 VAL H 20 ? LEU H 32 ? VAL H 167 LEU H 179 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N VAL A 15 ? N VAL A 162 O GLN B 14 ? O GLN B 161 AA1 2 3 N VAL B 15 ? N VAL B 162 O GLN C 14 ? O GLN C 161 AA1 3 4 N VAL C 15 ? N VAL C 162 O GLN D 14 ? O GLN D 161 AA2 1 2 N GLY A 22 ? N GLY A 169 O SER B 21 ? O SER B 168 AA2 2 3 N GLY B 22 ? N GLY B 169 O SER C 21 ? O SER C 168 AA2 3 4 N VAL C 20 ? N VAL C 167 O SER D 21 ? O SER D 168 AA3 1 2 N VAL E 15 ? N VAL E 162 O GLN F 14 ? O GLN F 161 AA3 2 3 N VAL F 15 ? N VAL F 162 O GLN G 14 ? O GLN G 161 AA3 3 4 N VAL G 15 ? N VAL G 162 O LEU H 16 ? O LEU H 163 AA4 1 2 N VAL E 20 ? N VAL E 167 O SER F 21 ? O SER F 168 AA4 2 3 N VAL F 20 ? N VAL F 167 O SER G 21 ? O SER G 168 AA4 3 4 N GLY G 22 ? N GLY G 169 O SER H 21 ? O SER H 168 # _pdbx_entry_details.entry_id 9JST _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9JST _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 9JST _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 1.79 _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 286491 _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 4.4 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type CELL _em_entity_assembly.name 'Wild-type native PMEL amyloid extracted from melanoma cell line' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9JST _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 2.7 _em_imaging.nominal_defocus_min 500 _em_imaging.nominal_defocus_max 2000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification 60000 _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 'COMA FREE' _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen NITROGEN # _em_sample_support.id 1 _em_sample_support.film_material ? _em_sample_support.method ? _em_sample_support.grid_material GOLD _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'UltrAuFoil R1.2/1.3' _em_sample_support.details ? _em_sample_support.specimen_id 1 _em_sample_support.citation_id ? # _em_vitrification.entry_id 9JST _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 100 _em_vitrification.temp ? _em_vitrification.chamber_temperature 283 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9JST _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state FILAMENT _em_experiment.entity_assembly_id 1 # 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 GLN N N N N 41 GLN CA C N S 42 GLN C C N N 43 GLN O O N N 44 GLN CB C N N 45 GLN CG C N N 46 GLN CD C N N 47 GLN OE1 O N N 48 GLN NE2 N N N 49 GLN OXT O N N 50 GLN H H N N 51 GLN H2 H N N 52 GLN HA H N N 53 GLN HB2 H N N 54 GLN HB3 H N N 55 GLN HG2 H N N 56 GLN HG3 H N N 57 GLN HE21 H N N 58 GLN HE22 H N N 59 GLN HXT H N N 60 GLY N N N N 61 GLY CA C N N 62 GLY C C N N 63 GLY O O N N 64 GLY OXT O N N 65 GLY H H N N 66 GLY H2 H N N 67 GLY HA2 H N N 68 GLY HA3 H N N 69 GLY HXT H N N 70 HIS N N N N 71 HIS CA C N S 72 HIS C C N N 73 HIS O O N N 74 HIS CB C N N 75 HIS CG C Y N 76 HIS ND1 N Y N 77 HIS CD2 C Y N 78 HIS CE1 C Y N 79 HIS NE2 N Y N 80 HIS OXT O N N 81 HIS H H N N 82 HIS H2 H N N 83 HIS HA H N N 84 HIS HB2 H N N 85 HIS HB3 H N N 86 HIS HD1 H N N 87 HIS HD2 H N N 88 HIS HE1 H N N 89 HIS HE2 H N N 90 HIS HXT H N N 91 ILE N N N N 92 ILE CA C N S 93 ILE C C N N 94 ILE O O N N 95 ILE CB C N S 96 ILE CG1 C N N 97 ILE CG2 C N N 98 ILE CD1 C N N 99 ILE OXT O N N 100 ILE H H N N 101 ILE H2 H N N 102 ILE HA H N N 103 ILE HB H N N 104 ILE HG12 H N N 105 ILE HG13 H N N 106 ILE HG21 H N N 107 ILE HG22 H N N 108 ILE HG23 H N N 109 ILE HD11 H N N 110 ILE HD12 H N N 111 ILE HD13 H N N 112 ILE HXT H N N 113 LEU N N N N 114 LEU CA C N S 115 LEU C C N N 116 LEU O O N N 117 LEU CB C N N 118 LEU CG C N N 119 LEU CD1 C N N 120 LEU CD2 C N N 121 LEU OXT O N N 122 LEU H H N N 123 LEU H2 H N N 124 LEU HA H N N 125 LEU HB2 H N N 126 LEU HB3 H N N 127 LEU HG H N N 128 LEU HD11 H N N 129 LEU HD12 H N N 130 LEU HD13 H N N 131 LEU HD21 H N N 132 LEU HD22 H N N 133 LEU HD23 H N N 134 LEU HXT H N N 135 LYS N N N N 136 LYS CA C N S 137 LYS C C N N 138 LYS O O N N 139 LYS CB C N N 140 LYS CG C N N 141 LYS CD C N N 142 LYS CE C N N 143 LYS NZ N N N 144 LYS OXT O N N 145 LYS H H N N 146 LYS H2 H N N 147 LYS HA H N N 148 LYS HB2 H N N 149 LYS HB3 H N N 150 LYS HG2 H N N 151 LYS HG3 H N N 152 LYS HD2 H N N 153 LYS HD3 H N N 154 LYS HE2 H N N 155 LYS HE3 H N N 156 LYS HZ1 H N N 157 LYS HZ2 H N N 158 LYS HZ3 H N N 159 LYS HXT H N N 160 MET N N N N 161 MET CA C N S 162 MET C C N N 163 MET O O N N 164 MET CB C N N 165 MET CG C N N 166 MET SD S N N 167 MET CE C N N 168 MET OXT O N N 169 MET H H N N 170 MET H2 H N N 171 MET HA H N N 172 MET HB2 H N N 173 MET HB3 H N N 174 MET HG2 H N N 175 MET HG3 H N N 176 MET HE1 H N N 177 MET HE2 H N N 178 MET HE3 H N N 179 MET HXT H N N 180 PHE N N N N 181 PHE CA C N S 182 PHE C C N N 183 PHE O O N N 184 PHE CB C N N 185 PHE CG C Y N 186 PHE CD1 C Y N 187 PHE CD2 C Y N 188 PHE CE1 C Y N 189 PHE CE2 C Y N 190 PHE CZ C Y N 191 PHE OXT O N N 192 PHE H H N N 193 PHE H2 H N N 194 PHE HA H N N 195 PHE HB2 H N N 196 PHE HB3 H N N 197 PHE HD1 H N N 198 PHE HD2 H N N 199 PHE HE1 H N N 200 PHE HE2 H N N 201 PHE HZ H N N 202 PHE HXT H N N 203 PRO N N N N 204 PRO CA C N S 205 PRO C C N N 206 PRO O O N N 207 PRO CB C N N 208 PRO CG C N N 209 PRO CD C N N 210 PRO OXT O N N 211 PRO H H N N 212 PRO HA H N N 213 PRO HB2 H N N 214 PRO HB3 H N N 215 PRO HG2 H N N 216 PRO HG3 H N N 217 PRO HD2 H N N 218 PRO HD3 H N N 219 PRO HXT H N N 220 SER N N N N 221 SER CA C N S 222 SER C C N N 223 SER O O N N 224 SER CB C N N 225 SER OG O N N 226 SER OXT O N N 227 SER H H N N 228 SER H2 H N N 229 SER HA H N N 230 SER HB2 H N N 231 SER HB3 H N N 232 SER HG H N N 233 SER HXT H N N 234 THR N N N N 235 THR CA C N S 236 THR C C N N 237 THR O O N N 238 THR CB C N R 239 THR OG1 O N N 240 THR CG2 C N N 241 THR OXT O N N 242 THR H H N N 243 THR H2 H N N 244 THR HA H N N 245 THR HB H N N 246 THR HG1 H N N 247 THR HG21 H N N 248 THR HG22 H N N 249 THR HG23 H N N 250 THR HXT H N N 251 TRP N N N N 252 TRP CA C N S 253 TRP C C N N 254 TRP O O N N 255 TRP CB C N N 256 TRP CG C Y N 257 TRP CD1 C Y N 258 TRP CD2 C Y N 259 TRP NE1 N Y N 260 TRP CE2 C Y N 261 TRP CE3 C Y N 262 TRP CZ2 C Y N 263 TRP CZ3 C Y N 264 TRP CH2 C Y N 265 TRP OXT O N N 266 TRP H H N N 267 TRP H2 H N N 268 TRP HA H N N 269 TRP HB2 H N N 270 TRP HB3 H N N 271 TRP HD1 H N N 272 TRP HE1 H N N 273 TRP HE3 H N N 274 TRP HZ2 H N N 275 TRP HZ3 H N N 276 TRP HH2 H N N 277 TRP HXT H N N 278 TYR N N N N 279 TYR CA C N S 280 TYR C C N N 281 TYR O O N N 282 TYR CB C N N 283 TYR CG C Y N 284 TYR CD1 C Y N 285 TYR CD2 C Y N 286 TYR CE1 C Y N 287 TYR CE2 C Y N 288 TYR CZ C Y N 289 TYR OH O N N 290 TYR OXT O N N 291 TYR H H N N 292 TYR H2 H N N 293 TYR HA H N N 294 TYR HB2 H N N 295 TYR HB3 H N N 296 TYR HD1 H N N 297 TYR HD2 H N N 298 TYR HE1 H N N 299 TYR HE2 H N N 300 TYR HH H N N 301 TYR HXT H N N 302 VAL N N N N 303 VAL CA C N S 304 VAL C C N N 305 VAL O O N N 306 VAL CB C N N 307 VAL CG1 C N N 308 VAL CG2 C N N 309 VAL OXT O N N 310 VAL H H N N 311 VAL H2 H N N 312 VAL HA H N N 313 VAL HB H N N 314 VAL HG11 H N N 315 VAL HG12 H N N 316 VAL HG13 H N N 317 VAL HG21 H N N 318 VAL HG22 H N N 319 VAL HG23 H N N 320 VAL HXT H N N 321 # 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 GLN N CA sing N N 39 GLN N H sing N N 40 GLN N H2 sing N N 41 GLN CA C sing N N 42 GLN CA CB sing N N 43 GLN CA HA sing N N 44 GLN C O doub N N 45 GLN C OXT sing N N 46 GLN CB CG sing N N 47 GLN CB HB2 sing N N 48 GLN CB HB3 sing N N 49 GLN CG CD sing N N 50 GLN CG HG2 sing N N 51 GLN CG HG3 sing N N 52 GLN CD OE1 doub N N 53 GLN CD NE2 sing N N 54 GLN NE2 HE21 sing N N 55 GLN NE2 HE22 sing N N 56 GLN OXT HXT sing N N 57 GLY N CA sing N N 58 GLY N H sing N N 59 GLY N H2 sing N N 60 GLY CA C sing N N 61 GLY CA HA2 sing N N 62 GLY CA HA3 sing N N 63 GLY C O doub N N 64 GLY C OXT sing N N 65 GLY OXT HXT sing N N 66 HIS N CA sing N N 67 HIS N H sing N N 68 HIS N H2 sing N N 69 HIS CA C sing N N 70 HIS CA CB sing N N 71 HIS CA HA sing N N 72 HIS C O doub N N 73 HIS C OXT sing N N 74 HIS CB CG sing N N 75 HIS CB HB2 sing N N 76 HIS CB HB3 sing N N 77 HIS CG ND1 sing Y N 78 HIS CG CD2 doub Y N 79 HIS ND1 CE1 doub Y N 80 HIS ND1 HD1 sing N N 81 HIS CD2 NE2 sing Y N 82 HIS CD2 HD2 sing N N 83 HIS CE1 NE2 sing Y N 84 HIS CE1 HE1 sing N N 85 HIS NE2 HE2 sing N N 86 HIS OXT HXT sing N N 87 ILE N CA sing N N 88 ILE N H sing N N 89 ILE N H2 sing N N 90 ILE CA C sing N N 91 ILE CA CB sing N N 92 ILE CA HA sing N N 93 ILE C O doub N N 94 ILE C OXT sing N N 95 ILE CB CG1 sing N N 96 ILE CB CG2 sing N N 97 ILE CB HB sing N N 98 ILE CG1 CD1 sing N N 99 ILE CG1 HG12 sing N N 100 ILE CG1 HG13 sing N N 101 ILE CG2 HG21 sing N N 102 ILE CG2 HG22 sing N N 103 ILE CG2 HG23 sing N N 104 ILE CD1 HD11 sing N N 105 ILE CD1 HD12 sing N N 106 ILE CD1 HD13 sing N N 107 ILE OXT HXT sing N N 108 LEU N CA sing N N 109 LEU N H sing N N 110 LEU N H2 sing N N 111 LEU CA C sing N N 112 LEU CA CB sing N N 113 LEU CA HA sing N N 114 LEU C O doub N N 115 LEU C OXT sing N N 116 LEU CB CG sing N N 117 LEU CB HB2 sing N N 118 LEU CB HB3 sing N N 119 LEU CG CD1 sing N N 120 LEU CG CD2 sing N N 121 LEU CG HG sing N N 122 LEU CD1 HD11 sing N N 123 LEU CD1 HD12 sing N N 124 LEU CD1 HD13 sing N N 125 LEU CD2 HD21 sing N N 126 LEU CD2 HD22 sing N N 127 LEU CD2 HD23 sing N N 128 LEU OXT HXT sing N N 129 LYS N CA sing N N 130 LYS N H sing N N 131 LYS N H2 sing N N 132 LYS CA C sing N N 133 LYS CA CB sing N N 134 LYS CA HA sing N N 135 LYS C O doub N N 136 LYS C OXT sing N N 137 LYS CB CG sing N N 138 LYS CB HB2 sing N N 139 LYS CB HB3 sing N N 140 LYS CG CD sing N N 141 LYS CG HG2 sing N N 142 LYS CG HG3 sing N N 143 LYS CD CE sing N N 144 LYS CD HD2 sing N N 145 LYS CD HD3 sing N N 146 LYS CE NZ sing N N 147 LYS CE HE2 sing N N 148 LYS CE HE3 sing N N 149 LYS NZ HZ1 sing N N 150 LYS NZ HZ2 sing N N 151 LYS NZ HZ3 sing N N 152 LYS OXT HXT sing N N 153 MET N CA sing N N 154 MET N H sing N N 155 MET N H2 sing N N 156 MET CA C sing N N 157 MET CA CB sing N N 158 MET CA HA sing N N 159 MET C O doub N N 160 MET C OXT sing N N 161 MET CB CG sing N N 162 MET CB HB2 sing N N 163 MET CB HB3 sing N N 164 MET CG SD sing N N 165 MET CG HG2 sing N N 166 MET CG HG3 sing N N 167 MET SD CE sing N N 168 MET CE HE1 sing N N 169 MET CE HE2 sing N N 170 MET CE HE3 sing N N 171 MET OXT HXT sing N N 172 PHE N CA sing N N 173 PHE N H sing N N 174 PHE N H2 sing N N 175 PHE CA C sing N N 176 PHE CA CB sing N N 177 PHE CA HA sing N N 178 PHE C O doub N N 179 PHE C OXT sing N N 180 PHE CB CG sing N N 181 PHE CB HB2 sing N N 182 PHE CB HB3 sing N N 183 PHE CG CD1 doub Y N 184 PHE CG CD2 sing Y N 185 PHE CD1 CE1 sing Y N 186 PHE CD1 HD1 sing N N 187 PHE CD2 CE2 doub Y N 188 PHE CD2 HD2 sing N N 189 PHE CE1 CZ doub Y N 190 PHE CE1 HE1 sing N N 191 PHE CE2 CZ sing Y N 192 PHE CE2 HE2 sing N N 193 PHE CZ HZ sing N N 194 PHE OXT HXT sing N N 195 PRO N CA sing N N 196 PRO N CD sing N N 197 PRO N H sing N N 198 PRO CA C sing N N 199 PRO CA CB sing N N 200 PRO CA HA sing N N 201 PRO C O doub N N 202 PRO C OXT sing N N 203 PRO CB CG sing N N 204 PRO CB HB2 sing N N 205 PRO CB HB3 sing N N 206 PRO CG CD sing N N 207 PRO CG HG2 sing N N 208 PRO CG HG3 sing N N 209 PRO CD HD2 sing N N 210 PRO CD HD3 sing N N 211 PRO OXT HXT sing N N 212 SER N CA sing N N 213 SER N H sing N N 214 SER N H2 sing N N 215 SER CA C sing N N 216 SER CA CB sing N N 217 SER CA HA sing N N 218 SER C O doub N N 219 SER C OXT sing N N 220 SER CB OG sing N N 221 SER CB HB2 sing N N 222 SER CB HB3 sing N N 223 SER OG HG sing N N 224 SER OXT HXT sing N N 225 THR N CA sing N N 226 THR N H sing N N 227 THR N H2 sing N N 228 THR CA C sing N N 229 THR CA CB sing N N 230 THR CA HA sing N N 231 THR C O doub N N 232 THR C OXT sing N N 233 THR CB OG1 sing N N 234 THR CB CG2 sing N N 235 THR CB HB sing N N 236 THR OG1 HG1 sing N N 237 THR CG2 HG21 sing N N 238 THR CG2 HG22 sing N N 239 THR CG2 HG23 sing N N 240 THR OXT HXT sing N N 241 TRP N CA sing N N 242 TRP N H sing N N 243 TRP N H2 sing N N 244 TRP CA C sing N N 245 TRP CA CB sing N N 246 TRP CA HA sing N N 247 TRP C O doub N N 248 TRP C OXT sing N N 249 TRP CB CG sing N N 250 TRP CB HB2 sing N N 251 TRP CB HB3 sing N N 252 TRP CG CD1 doub Y N 253 TRP CG CD2 sing Y N 254 TRP CD1 NE1 sing Y N 255 TRP CD1 HD1 sing N N 256 TRP CD2 CE2 doub Y N 257 TRP CD2 CE3 sing Y N 258 TRP NE1 CE2 sing Y N 259 TRP NE1 HE1 sing N N 260 TRP CE2 CZ2 sing Y N 261 TRP CE3 CZ3 doub Y N 262 TRP CE3 HE3 sing N N 263 TRP CZ2 CH2 doub Y N 264 TRP CZ2 HZ2 sing N N 265 TRP CZ3 CH2 sing Y N 266 TRP CZ3 HZ3 sing N N 267 TRP CH2 HH2 sing N N 268 TRP OXT HXT sing N N 269 TYR N CA sing N N 270 TYR N H sing N N 271 TYR N H2 sing N N 272 TYR CA C sing N N 273 TYR CA CB sing N N 274 TYR CA HA sing N N 275 TYR C O doub N N 276 TYR C OXT sing N N 277 TYR CB CG sing N N 278 TYR CB HB2 sing N N 279 TYR CB HB3 sing N N 280 TYR CG CD1 doub Y N 281 TYR CG CD2 sing Y N 282 TYR CD1 CE1 sing Y N 283 TYR CD1 HD1 sing N N 284 TYR CD2 CE2 doub Y N 285 TYR CD2 HD2 sing N N 286 TYR CE1 CZ doub Y N 287 TYR CE1 HE1 sing N N 288 TYR CE2 CZ sing Y N 289 TYR CE2 HE2 sing N N 290 TYR CZ OH sing N N 291 TYR OH HH sing N N 292 TYR OXT HXT sing N N 293 VAL N CA sing N N 294 VAL N H sing N N 295 VAL N H2 sing N N 296 VAL CA C sing N N 297 VAL CA CB sing N N 298 VAL CA HA sing N N 299 VAL C O doub N N 300 VAL C OXT sing N N 301 VAL CB CG1 sing N N 302 VAL CB CG2 sing N N 303 VAL CB HB sing N N 304 VAL CG1 HG11 sing N N 305 VAL CG1 HG12 sing N N 306 VAL CG1 HG13 sing N N 307 VAL CG2 HG21 sing N N 308 VAL CG2 HG22 sing N N 309 VAL CG2 HG23 sing N N 310 VAL OXT HXT sing N N 311 # _em_admin.current_status REL _em_admin.deposition_date 2024-10-01 _em_admin.deposition_site PDBJ _em_admin.entry_id 9JST _em_admin.last_update 2024-10-09 _em_admin.map_release_date 2024-10-09 _em_admin.title 'Wild-type native PMEL amyloid - polymorph 1' # _em_buffer_component.buffer_id 1 _em_buffer_component.concentration 150 _em_buffer_component.concentration_units mM _em_buffer_component.formula CH3COONa _em_buffer_component.id 1 _em_buffer_component.name 'Sodium acetate' # _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_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 9606 _em_entity_assembly_naturalsource.organism 'Homo sapiens' _em_entity_assembly_naturalsource.organelle Melanosome _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time 5.5 _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 50 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k 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 ? # _em_imaging_optics.chr_aberration_corrector ? _em_imaging_optics.energyfilter_lower ? _em_imaging_optics.energyfilter_slit_width 20 _em_imaging_optics.energyfilter_name 'In-column Omega Filter' _em_imaging_optics.energyfilter_upper ? _em_imaging_optics.id 1 _em_imaging_optics.imaging_id 1 _em_imaging_optics.phase_plate ? _em_imaging_optics.sph_aberration_corrector ? _em_imaging_optics.details ? # 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 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? 'VOLUME SELECTION' ? 14 1 1 1 ? ? 'SERIES ALIGNMENT' ? 15 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 16 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 17 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 18 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 19 1 1 1 ? ? # _em_specimen.concentration 0.3 _em_specimen.details 'This sample was monodisperse.' _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 24H02285 1 'Human Frontier Science Program (HFSP)' France RGP006/2023 2 # _atom_sites.entry_id 9JST _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 H N O S # loop_