data_8ACB # _entry.id 8ACB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.370 _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 8ACB pdb_00008acb 10.2210/pdb8acb/pdb WWPDB D_1292123941 ? ? EMDB EMD-15345 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'CryoEM structure of sweet potato feathery mottle virus VLP' _pdbx_database_related.db_id EMD-15345 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8ACB _pdbx_database_status.recvd_initial_deposition_date 2022-07-05 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category FoldIt _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Javed, A.' 1 ? 'Byrne, J.M.' 2 ? 'Ranson, N.' 3 ? 'Lomonosoff, G.' 4 ? # _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 'Commun Biol' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2399-3642 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 6 _citation.language ? _citation.page_first 433 _citation.page_last 433 _citation.title 'CryoEM and stability analysis of virus-like particles of potyvirus and ipomovirus infecting a common host.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s42003-023-04799-x _citation.pdbx_database_id_PubMed 37076658 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chase, O.' 1 ? primary 'Javed, A.' 2 ? primary 'Byrne, M.J.' 3 ? primary 'Thuenemann, E.C.' 4 ? primary 'Lomonossoff, G.P.' 5 0000-0003-0700-906X primary 'Ranson, N.A.' 6 0000-0002-3640-5275 primary 'Lopez-Moya, J.J.' 7 0000-0002-3176-9651 # _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 8ACB _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 8ACB _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 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Genome polyprotein' 25209.426 1 ? ? ? ? 2 polymer nat 'Single-stranded RNA' 1485.872 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;VPRVKMNANKKRQPMVNGRAIINFQHLSTYEPEQFEVANTRSTQEQFQAWYEGVKGDYGVDDTGMGILLNGLMVWCIENG TSPNINGVWTMMDGDEQVTYPIKPLLDHAVPTFRQIMTHFSDVAEAYIEMRNRTKAYMPRYGLQRNLTDMSLARYAFDFY ELHSTTPARAKEAHLQMKAAALKNARNRLFGLDGNVSTQEEDTERHTTTDVTRNIHNLLG ; ;VPRVKMNANKKRQPMVNGRAIINFQHLSTYEPEQFEVANTRSTQEQFQAWYEGVKGDYGVDDTGMGILLNGLMVWCIENG TSPNINGVWTMMDGDEQVTYPIKPLLDHAVPTFRQIMTHFSDVAEAYIEMRNRTKAYMPRYGLQRNLTDMSLARYAFDFY ELHSTTPARAKEAHLQMKAAALKNARNRLFGLDGNVSTQEEDTERHTTTDVTRNIHNLLG ; A ? 2 polyribonucleotide no no UUUUU UUUUU B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 VAL n 1 2 PRO n 1 3 ARG n 1 4 VAL n 1 5 LYS n 1 6 MET n 1 7 ASN n 1 8 ALA n 1 9 ASN n 1 10 LYS n 1 11 LYS n 1 12 ARG n 1 13 GLN n 1 14 PRO n 1 15 MET n 1 16 VAL n 1 17 ASN n 1 18 GLY n 1 19 ARG n 1 20 ALA n 1 21 ILE n 1 22 ILE n 1 23 ASN n 1 24 PHE n 1 25 GLN n 1 26 HIS n 1 27 LEU n 1 28 SER n 1 29 THR n 1 30 TYR n 1 31 GLU n 1 32 PRO n 1 33 GLU n 1 34 GLN n 1 35 PHE n 1 36 GLU n 1 37 VAL n 1 38 ALA n 1 39 ASN n 1 40 THR n 1 41 ARG n 1 42 SER n 1 43 THR n 1 44 GLN n 1 45 GLU n 1 46 GLN n 1 47 PHE n 1 48 GLN n 1 49 ALA n 1 50 TRP n 1 51 TYR n 1 52 GLU n 1 53 GLY n 1 54 VAL n 1 55 LYS n 1 56 GLY n 1 57 ASP n 1 58 TYR n 1 59 GLY n 1 60 VAL n 1 61 ASP n 1 62 ASP n 1 63 THR n 1 64 GLY n 1 65 MET n 1 66 GLY n 1 67 ILE n 1 68 LEU n 1 69 LEU n 1 70 ASN n 1 71 GLY n 1 72 LEU n 1 73 MET n 1 74 VAL n 1 75 TRP n 1 76 CYS n 1 77 ILE n 1 78 GLU n 1 79 ASN n 1 80 GLY n 1 81 THR n 1 82 SER n 1 83 PRO n 1 84 ASN n 1 85 ILE n 1 86 ASN n 1 87 GLY n 1 88 VAL n 1 89 TRP n 1 90 THR n 1 91 MET n 1 92 MET n 1 93 ASP n 1 94 GLY n 1 95 ASP n 1 96 GLU n 1 97 GLN n 1 98 VAL n 1 99 THR n 1 100 TYR n 1 101 PRO n 1 102 ILE n 1 103 LYS n 1 104 PRO n 1 105 LEU n 1 106 LEU n 1 107 ASP n 1 108 HIS n 1 109 ALA n 1 110 VAL n 1 111 PRO n 1 112 THR n 1 113 PHE n 1 114 ARG n 1 115 GLN n 1 116 ILE n 1 117 MET n 1 118 THR n 1 119 HIS n 1 120 PHE n 1 121 SER n 1 122 ASP n 1 123 VAL n 1 124 ALA n 1 125 GLU n 1 126 ALA n 1 127 TYR n 1 128 ILE n 1 129 GLU n 1 130 MET n 1 131 ARG n 1 132 ASN n 1 133 ARG n 1 134 THR n 1 135 LYS n 1 136 ALA n 1 137 TYR n 1 138 MET n 1 139 PRO n 1 140 ARG n 1 141 TYR n 1 142 GLY n 1 143 LEU n 1 144 GLN n 1 145 ARG n 1 146 ASN n 1 147 LEU n 1 148 THR n 1 149 ASP n 1 150 MET n 1 151 SER n 1 152 LEU n 1 153 ALA n 1 154 ARG n 1 155 TYR n 1 156 ALA n 1 157 PHE n 1 158 ASP n 1 159 PHE n 1 160 TYR n 1 161 GLU n 1 162 LEU n 1 163 HIS n 1 164 SER n 1 165 THR n 1 166 THR n 1 167 PRO n 1 168 ALA n 1 169 ARG n 1 170 ALA n 1 171 LYS n 1 172 GLU n 1 173 ALA n 1 174 HIS n 1 175 LEU n 1 176 GLN n 1 177 MET n 1 178 LYS n 1 179 ALA n 1 180 ALA n 1 181 ALA n 1 182 LEU n 1 183 LYS n 1 184 ASN n 1 185 ALA n 1 186 ARG n 1 187 ASN n 1 188 ARG n 1 189 LEU n 1 190 PHE n 1 191 GLY n 1 192 LEU n 1 193 ASP n 1 194 GLY n 1 195 ASN n 1 196 VAL n 1 197 SER n 1 198 THR n 1 199 GLN n 1 200 GLU n 1 201 GLU n 1 202 ASP n 1 203 THR n 1 204 GLU n 1 205 ARG n 1 206 HIS n 1 207 THR n 1 208 THR n 1 209 THR n 1 210 ASP n 1 211 VAL n 1 212 THR n 1 213 ARG n 1 214 ASN n 1 215 ILE n 1 216 HIS n 1 217 ASN n 1 218 LEU n 1 219 LEU n 1 220 GLY n 2 1 U n 2 2 U n 2 3 U n 2 4 U n 2 5 U 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 220 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _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 'Sweet potato feathery mottle virus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 12844 _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 'Nicotiana benthamiana' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 4100 _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 ? # _entity_src_nat.entity_id 2 _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 5 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Ipomoea batatas' _entity_src_nat.pdbx_ncbi_taxonomy_id 4120 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _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 ? _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_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 UNP D2CTM1_9POTV D2CTM1 ? 1 ;VPRVKMNANKKRQPMVNGRAIINFQHLSTYEPEQFEVANTRSTQEQFQAWYEGVKGDYGVDDTGMGILLNGLMVWCIENG TSPNINGVWTMMDGDEQVTYPIKPLLDHAVPTFRQIMTHFSDVAEAYIEMRNRTKAYMPRYGLQRNLTDMSLARYAFDFY ELHSTTPARAKEAHLQMKAAALKNARNRLFGLDGNVSTQEEDTERHTTTDVTRNIHNLLG ; 146 2 PDB 8ACB 8ACB ? 2 ? 1 # 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 8ACB A 1 ? 220 ? D2CTM1 146 ? 365 ? 91 310 2 2 8ACB B 1 ? 5 ? 8ACB 1 ? 5 ? 1 5 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _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 8ACB _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 43.42 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8ACB _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high . _refine.ls_d_res_low ? _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work ? _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method NONE _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # 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' ? 0.0019 ? 1860 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.4601 ? 2543 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.0342 ? 284 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.0028 ? 321 ? f_plane_restr ? ? 'ELECTRON MICROSCOPY' ? 7.7721 ? 298 ? f_dihedral_angle_d ? ? # _struct.entry_id 8ACB _struct.title 'CryoEM structure of sweet potato feathery mottle virus VLP' _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 8ACB _struct_keywords.text 'plant virus, coat protein, VIRUS LIKE PARTICLE' _struct_keywords.pdbx_keywords 'VIRUS LIKE PARTICLE' # 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 2 ? # 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 ASN A 23 ? TYR A 30 ? ASN A 113 TYR A 120 1 ? 8 HELX_P HELX_P2 AA2 GLU A 33 ? ALA A 38 ? GLU A 123 ALA A 128 5 ? 6 HELX_P HELX_P3 AA3 THR A 43 ? GLY A 59 ? THR A 133 GLY A 149 1 ? 17 HELX_P HELX_P4 AA4 ASP A 61 ? ASN A 79 ? ASP A 151 ASN A 169 1 ? 19 HELX_P HELX_P5 AA5 ILE A 102 ? HIS A 108 ? ILE A 192 HIS A 198 1 ? 7 HELX_P HELX_P6 AA6 THR A 112 ? HIS A 119 ? THR A 202 HIS A 209 1 ? 8 HELX_P HELX_P7 AA7 PHE A 120 ? ASN A 132 ? PHE A 210 ASN A 222 1 ? 13 HELX_P HELX_P8 AA8 PRO A 139 ? ARG A 145 ? PRO A 229 ARG A 235 1 ? 7 HELX_P HELX_P9 AA9 MET A 150 ? ARG A 154 ? MET A 240 ARG A 244 5 ? 5 HELX_P HELX_P10 AB1 ARG A 169 ? LEU A 182 ? ARG A 259 LEU A 272 1 ? 14 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id AA1 _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense anti-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 VAL A 88 ? ASP A 93 ? VAL A 178 ASP A 183 AA1 2 GLU A 96 ? PRO A 101 ? GLU A 186 PRO A 191 # _pdbx_struct_sheet_hbond.sheet_id AA1 _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id TRP _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 89 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id TRP _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 179 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id TYR _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 100 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id TYR _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 190 # _atom_sites.entry_id 8ACB _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.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 P S # 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 VAL 1 91 91 VAL VAL A . n A 1 2 PRO 2 92 92 PRO PRO A . n A 1 3 ARG 3 93 93 ARG ARG A . n A 1 4 VAL 4 94 94 VAL VAL A . n A 1 5 LYS 5 95 95 LYS LYS A . n A 1 6 MET 6 96 96 MET ALA A . n A 1 7 ASN 7 97 97 ASN ASN A . n A 1 8 ALA 8 98 98 ALA ALA A . n A 1 9 ASN 9 99 99 ASN ASN A . n A 1 10 LYS 10 100 100 LYS ALA A . n A 1 11 LYS 11 101 101 LYS ALA A . n A 1 12 ARG 12 102 102 ARG ALA A . n A 1 13 GLN 13 103 103 GLN GLN A . n A 1 14 PRO 14 104 104 PRO PRO A . n A 1 15 MET 15 105 105 MET MET A . n A 1 16 VAL 16 106 106 VAL VAL A . n A 1 17 ASN 17 107 107 ASN ASN A . n A 1 18 GLY 18 108 108 GLY GLY A . n A 1 19 ARG 19 109 109 ARG ARG A . n A 1 20 ALA 20 110 110 ALA ALA A . n A 1 21 ILE 21 111 111 ILE ILE A . n A 1 22 ILE 22 112 112 ILE ILE A . n A 1 23 ASN 23 113 113 ASN ASN A . n A 1 24 PHE 24 114 114 PHE PHE A . n A 1 25 GLN 25 115 115 GLN GLN A . n A 1 26 HIS 26 116 116 HIS HIS A . n A 1 27 LEU 27 117 117 LEU LEU A . n A 1 28 SER 28 118 118 SER SER A . n A 1 29 THR 29 119 119 THR THR A . n A 1 30 TYR 30 120 120 TYR TYR A . n A 1 31 GLU 31 121 121 GLU GLU A . n A 1 32 PRO 32 122 122 PRO PRO A . n A 1 33 GLU 33 123 123 GLU GLU A . n A 1 34 GLN 34 124 124 GLN GLN A . n A 1 35 PHE 35 125 125 PHE PHE A . n A 1 36 GLU 36 126 126 GLU GLU A . n A 1 37 VAL 37 127 127 VAL VAL A . n A 1 38 ALA 38 128 128 ALA ALA A . n A 1 39 ASN 39 129 129 ASN ASN A . n A 1 40 THR 40 130 130 THR THR A . n A 1 41 ARG 41 131 131 ARG ARG A . n A 1 42 SER 42 132 132 SER SER A . n A 1 43 THR 43 133 133 THR THR A . n A 1 44 GLN 44 134 134 GLN GLN A . n A 1 45 GLU 45 135 135 GLU GLU A . n A 1 46 GLN 46 136 136 GLN GLN A . n A 1 47 PHE 47 137 137 PHE PHE A . n A 1 48 GLN 48 138 138 GLN GLN A . n A 1 49 ALA 49 139 139 ALA ALA A . n A 1 50 TRP 50 140 140 TRP TRP A . n A 1 51 TYR 51 141 141 TYR TYR A . n A 1 52 GLU 52 142 142 GLU GLU A . n A 1 53 GLY 53 143 143 GLY GLY A . n A 1 54 VAL 54 144 144 VAL VAL A . n A 1 55 LYS 55 145 145 LYS LYS A . n A 1 56 GLY 56 146 146 GLY GLY A . n A 1 57 ASP 57 147 147 ASP ASP A . n A 1 58 TYR 58 148 148 TYR TYR A . n A 1 59 GLY 59 149 149 GLY GLY A . n A 1 60 VAL 60 150 150 VAL VAL A . n A 1 61 ASP 61 151 151 ASP ASP A . n A 1 62 ASP 62 152 152 ASP ASP A . n A 1 63 THR 63 153 153 THR THR A . n A 1 64 GLY 64 154 154 GLY GLY A . n A 1 65 MET 65 155 155 MET MET A . n A 1 66 GLY 66 156 156 GLY GLY A . n A 1 67 ILE 67 157 157 ILE ILE A . n A 1 68 LEU 68 158 158 LEU LEU A . n A 1 69 LEU 69 159 159 LEU LEU A . n A 1 70 ASN 70 160 160 ASN ASN A . n A 1 71 GLY 71 161 161 GLY GLY A . n A 1 72 LEU 72 162 162 LEU LEU A . n A 1 73 MET 73 163 163 MET MET A . n A 1 74 VAL 74 164 164 VAL VAL A . n A 1 75 TRP 75 165 165 TRP TRP A . n A 1 76 CYS 76 166 166 CYS CYS A . n A 1 77 ILE 77 167 167 ILE ILE A . n A 1 78 GLU 78 168 168 GLU GLU A . n A 1 79 ASN 79 169 169 ASN ASN A . n A 1 80 GLY 80 170 170 GLY GLY A . n A 1 81 THR 81 171 171 THR THR A . n A 1 82 SER 82 172 172 SER SER A . n A 1 83 PRO 83 173 173 PRO PRO A . n A 1 84 ASN 84 174 174 ASN ASN A . n A 1 85 ILE 85 175 175 ILE ILE A . n A 1 86 ASN 86 176 176 ASN ASN A . n A 1 87 GLY 87 177 177 GLY GLY A . n A 1 88 VAL 88 178 178 VAL VAL A . n A 1 89 TRP 89 179 179 TRP TRP A . n A 1 90 THR 90 180 180 THR THR A . n A 1 91 MET 91 181 181 MET MET A . n A 1 92 MET 92 182 182 MET MET A . n A 1 93 ASP 93 183 183 ASP ASP A . n A 1 94 GLY 94 184 184 GLY GLY A . n A 1 95 ASP 95 185 185 ASP ASP A . n A 1 96 GLU 96 186 186 GLU GLU A . n A 1 97 GLN 97 187 187 GLN GLN A . n A 1 98 VAL 98 188 188 VAL VAL A . n A 1 99 THR 99 189 189 THR THR A . n A 1 100 TYR 100 190 190 TYR TYR A . n A 1 101 PRO 101 191 191 PRO PRO A . n A 1 102 ILE 102 192 192 ILE ILE A . n A 1 103 LYS 103 193 193 LYS LYS A . n A 1 104 PRO 104 194 194 PRO PRO A . n A 1 105 LEU 105 195 195 LEU LEU A . n A 1 106 LEU 106 196 196 LEU LEU A . n A 1 107 ASP 107 197 197 ASP ASP A . n A 1 108 HIS 108 198 198 HIS HIS A . n A 1 109 ALA 109 199 199 ALA ALA A . n A 1 110 VAL 110 200 200 VAL VAL A . n A 1 111 PRO 111 201 201 PRO PRO A . n A 1 112 THR 112 202 202 THR THR A . n A 1 113 PHE 113 203 203 PHE PHE A . n A 1 114 ARG 114 204 204 ARG ARG A . n A 1 115 GLN 115 205 205 GLN GLN A . n A 1 116 ILE 116 206 206 ILE ILE A . n A 1 117 MET 117 207 207 MET MET A . n A 1 118 THR 118 208 208 THR THR A . n A 1 119 HIS 119 209 209 HIS HIS A . n A 1 120 PHE 120 210 210 PHE PHE A . n A 1 121 SER 121 211 211 SER SER A . n A 1 122 ASP 122 212 212 ASP ASP A . n A 1 123 VAL 123 213 213 VAL VAL A . n A 1 124 ALA 124 214 214 ALA ALA A . n A 1 125 GLU 125 215 215 GLU GLU A . n A 1 126 ALA 126 216 216 ALA ALA A . n A 1 127 TYR 127 217 217 TYR TYR A . n A 1 128 ILE 128 218 218 ILE ILE A . n A 1 129 GLU 129 219 219 GLU GLU A . n A 1 130 MET 130 220 220 MET MET A . n A 1 131 ARG 131 221 221 ARG ARG A . n A 1 132 ASN 132 222 222 ASN ASN A . n A 1 133 ARG 133 223 223 ARG ARG A . n A 1 134 THR 134 224 224 THR THR A . n A 1 135 LYS 135 225 225 LYS LYS A . n A 1 136 ALA 136 226 226 ALA ALA A . n A 1 137 TYR 137 227 227 TYR TYR A . n A 1 138 MET 138 228 228 MET MET A . n A 1 139 PRO 139 229 229 PRO PRO A . n A 1 140 ARG 140 230 230 ARG ARG A . n A 1 141 TYR 141 231 231 TYR TYR A . n A 1 142 GLY 142 232 232 GLY GLY A . n A 1 143 LEU 143 233 233 LEU LEU A . n A 1 144 GLN 144 234 234 GLN GLN A . n A 1 145 ARG 145 235 235 ARG ARG A . n A 1 146 ASN 146 236 236 ASN ASN A . n A 1 147 LEU 147 237 237 LEU LEU A . n A 1 148 THR 148 238 238 THR THR A . n A 1 149 ASP 149 239 239 ASP ASP A . n A 1 150 MET 150 240 240 MET MET A . n A 1 151 SER 151 241 241 SER SER A . n A 1 152 LEU 152 242 242 LEU LEU A . n A 1 153 ALA 153 243 243 ALA ALA A . n A 1 154 ARG 154 244 244 ARG ARG A . n A 1 155 TYR 155 245 245 TYR TYR A . n A 1 156 ALA 156 246 246 ALA ALA A . n A 1 157 PHE 157 247 247 PHE PHE A . n A 1 158 ASP 158 248 248 ASP ASP A . n A 1 159 PHE 159 249 249 PHE PHE A . n A 1 160 TYR 160 250 250 TYR TYR A . n A 1 161 GLU 161 251 251 GLU GLU A . n A 1 162 LEU 162 252 252 LEU LEU A . n A 1 163 HIS 163 253 253 HIS HIS A . n A 1 164 SER 164 254 254 SER SER A . n A 1 165 THR 165 255 255 THR THR A . n A 1 166 THR 166 256 256 THR THR A . n A 1 167 PRO 167 257 257 PRO PRO A . n A 1 168 ALA 168 258 258 ALA ALA A . n A 1 169 ARG 169 259 259 ARG ARG A . n A 1 170 ALA 170 260 260 ALA ALA A . n A 1 171 LYS 171 261 261 LYS LYS A . n A 1 172 GLU 172 262 262 GLU GLU A . n A 1 173 ALA 173 263 263 ALA ALA A . n A 1 174 HIS 174 264 264 HIS HIS A . n A 1 175 LEU 175 265 265 LEU LEU A . n A 1 176 GLN 176 266 266 GLN GLN A . n A 1 177 MET 177 267 267 MET MET A . n A 1 178 LYS 178 268 268 LYS LYS A . n A 1 179 ALA 179 269 269 ALA ALA A . n A 1 180 ALA 180 270 270 ALA ALA A . n A 1 181 ALA 181 271 271 ALA ALA A . n A 1 182 LEU 182 272 272 LEU LEU A . n A 1 183 LYS 183 273 273 LYS LYS A . n A 1 184 ASN 184 274 274 ASN ASN A . n A 1 185 ALA 185 275 275 ALA ALA A . n A 1 186 ARG 186 276 276 ARG ARG A . n A 1 187 ASN 187 277 277 ASN ASN A . n A 1 188 ARG 188 278 278 ARG ARG A . n A 1 189 LEU 189 279 279 LEU LEU A . n A 1 190 PHE 190 280 280 PHE PHE A . n A 1 191 GLY 191 281 281 GLY GLY A . n A 1 192 LEU 192 282 282 LEU LEU A . n A 1 193 ASP 193 283 283 ASP ASP A . n A 1 194 GLY 194 284 284 GLY GLY A . n A 1 195 ASN 195 285 285 ASN ASN A . n A 1 196 VAL 196 286 286 VAL VAL A . n A 1 197 SER 197 287 287 SER SER A . n A 1 198 THR 198 288 288 THR ALA A . n A 1 199 GLN 199 289 289 GLN ALA A . n A 1 200 GLU 200 290 290 GLU ALA A . n A 1 201 GLU 201 291 291 GLU GLU A . n A 1 202 ASP 202 292 292 ASP ASP A . n A 1 203 THR 203 293 293 THR THR A . n A 1 204 GLU 204 294 294 GLU GLU A . n A 1 205 ARG 205 295 295 ARG ARG A . n A 1 206 HIS 206 296 296 HIS ALA A . n A 1 207 THR 207 297 297 THR THR A . n A 1 208 THR 208 298 298 THR THR A . n A 1 209 THR 209 299 299 THR THR A . n A 1 210 ASP 210 300 300 ASP ASP A . n A 1 211 VAL 211 301 301 VAL VAL A . n A 1 212 THR 212 302 302 THR THR A . n A 1 213 ARG 213 303 303 ARG ALA A . n A 1 214 ASN 214 304 304 ASN ASN A . n A 1 215 ILE 215 305 305 ILE ALA A . n A 1 216 HIS 216 306 306 HIS ALA A . n A 1 217 ASN 217 307 307 ASN ALA A . n A 1 218 LEU 218 308 308 LEU LEU A . n A 1 219 LEU 219 309 309 LEU ALA A . n A 1 220 GLY 220 310 310 GLY GLY A . n B 2 1 U 1 1 1 U U B . n B 2 2 U 2 2 2 U U B . n B 2 3 U 3 3 3 U U B . n B 2 4 U 4 4 4 U U B . n B 2 5 U 5 5 5 U U B . n # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 5 juanjose.lopez@cragenomica.es Juan Lopez-Moya Jose 'principal investigator/group leader' 0000-0002-3176-9651 6 n.a.ranson@leeds.ac.uk Neil Ranson ? 'principal investigator/group leader' 0000-0002-3640-5275 7 george.lomonossoff@jic.ac.uk George Lomonosoff ? 'principal investigator/group leader' 0000-0003-0700-906X # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 # _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 2023-05-17 # _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 ? # _space_group_symop.id 1 _space_group_symop.operation_xyz x,y,z # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? phenix.real_space_refine ? ? ? 1.19.2_4158 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.19.2_4158 2 # _em_3d_fitting.entry_id 8ACB _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value 140.9 _em_3d_fitting.ref_protocol 'FLEXIBLE FIT' _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria 'Correlation coefficient' _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 8ACB _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm 'FOURIER SPACE' _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages 1 _em_3d_reconstruction.num_particles 48042 _em_3d_reconstruction.resolution 2.6 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type HELICAL _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'Sweet potato feathery mottle virus' _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type VIRUS _em_entity_assembly.entity_id_list '1, 2' _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 8ACB _em_image_scans.id 1 _em_image_scans.dimension_height ? _em_image_scans.dimension_width ? _em_image_scans.frames_per_image ? _em_image_scans.image_recording_id 1 _em_image_scans.sampling_size 14 _em_image_scans.scanner_model ? _em_image_scans.used_frames_per_image ? _em_image_scans.citation_id ? _em_image_scans.number_digital_images ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.details ? # _em_imaging.id 1 _em_imaging.entry_id 8ACB _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure 'ZEMLIN TABLEAU' _em_imaging.c2_aperture_diameter 70 _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max 3000 _em_imaging.nominal_defocus_min 800 _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'Quantifoil R1.2/1.3' _em_sample_support.method ? _em_sample_support.film_material ? # _em_virus_entity.entity_assembly_id 1 _em_virus_entity.empty NO _em_virus_entity.enveloped NO _em_virus_entity.virus_isolate SPECIES _em_virus_entity.virus_type 'VIRUS-LIKE PARTICLE' _em_virus_entity.id 1 _em_virus_entity.virus_host_category ? _em_virus_entity.details ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature 277 _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 100 _em_vitrification.instrument ? _em_vitrification.entry_id 8ACB _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 8ACB _em_experiment.id 1 _em_experiment.aggregation_state FILAMENT _em_experiment.reconstruction_method HELICAL _em_experiment.entity_assembly_id 1 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 U _pdbx_validate_rmsd_angle.auth_seq_id_1 1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "O3'" _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 U _pdbx_validate_rmsd_angle.auth_seq_id_2 1 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 P _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 U _pdbx_validate_rmsd_angle.auth_seq_id_3 2 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 109.93 _pdbx_validate_rmsd_angle.angle_target_value 119.70 _pdbx_validate_rmsd_angle.angle_deviation -9.77 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.20 _pdbx_validate_rmsd_angle.linker_flag Y # 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 LYS A 100 ? ? 60.14 -95.45 2 1 LYS A 101 ? ? 60.33 -105.11 3 1 GLN A 103 ? ? 65.61 152.47 4 1 ASN A 222 ? ? -95.31 59.95 5 1 LEU A 242 ? ? -90.96 49.31 6 1 ALA A 246 ? ? -142.81 28.99 7 1 SER A 287 ? ? 61.11 -117.21 8 1 THR A 288 ? ? 60.92 -155.26 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A MET 96 ? CG ? A MET 6 CG 2 1 Y 1 A MET 96 ? SD ? A MET 6 SD 3 1 Y 1 A MET 96 ? CE ? A MET 6 CE 4 1 Y 1 A LYS 100 ? CG ? A LYS 10 CG 5 1 Y 1 A LYS 100 ? CD ? A LYS 10 CD 6 1 Y 1 A LYS 100 ? CE ? A LYS 10 CE 7 1 Y 1 A LYS 100 ? NZ ? A LYS 10 NZ 8 1 Y 1 A LYS 101 ? CG ? A LYS 11 CG 9 1 Y 1 A LYS 101 ? CD ? A LYS 11 CD 10 1 Y 1 A LYS 101 ? CE ? A LYS 11 CE 11 1 Y 1 A LYS 101 ? NZ ? A LYS 11 NZ 12 1 Y 1 A ARG 102 ? CG ? A ARG 12 CG 13 1 Y 1 A ARG 102 ? CD ? A ARG 12 CD 14 1 Y 1 A ARG 102 ? NE ? A ARG 12 NE 15 1 Y 1 A ARG 102 ? CZ ? A ARG 12 CZ 16 1 Y 1 A ARG 102 ? NH1 ? A ARG 12 NH1 17 1 Y 1 A ARG 102 ? NH2 ? A ARG 12 NH2 18 1 Y 1 A THR 288 ? OG1 ? A THR 198 OG1 19 1 Y 1 A THR 288 ? CG2 ? A THR 198 CG2 20 1 Y 1 A GLN 289 ? CG ? A GLN 199 CG 21 1 Y 1 A GLN 289 ? CD ? A GLN 199 CD 22 1 Y 1 A GLN 289 ? OE1 ? A GLN 199 OE1 23 1 Y 1 A GLN 289 ? NE2 ? A GLN 199 NE2 24 1 Y 1 A GLU 290 ? CG ? A GLU 200 CG 25 1 Y 1 A GLU 290 ? CD ? A GLU 200 CD 26 1 Y 1 A GLU 290 ? OE1 ? A GLU 200 OE1 27 1 Y 1 A GLU 290 ? OE2 ? A GLU 200 OE2 28 1 Y 1 A HIS 296 ? CG ? A HIS 206 CG 29 1 Y 1 A HIS 296 ? ND1 ? A HIS 206 ND1 30 1 Y 1 A HIS 296 ? CD2 ? A HIS 206 CD2 31 1 Y 1 A HIS 296 ? CE1 ? A HIS 206 CE1 32 1 Y 1 A HIS 296 ? NE2 ? A HIS 206 NE2 33 1 Y 1 A ARG 303 ? CG ? A ARG 213 CG 34 1 Y 1 A ARG 303 ? CD ? A ARG 213 CD 35 1 Y 1 A ARG 303 ? NE ? A ARG 213 NE 36 1 Y 1 A ARG 303 ? CZ ? A ARG 213 CZ 37 1 Y 1 A ARG 303 ? NH1 ? A ARG 213 NH1 38 1 Y 1 A ARG 303 ? NH2 ? A ARG 213 NH2 39 1 Y 1 A ILE 305 ? CG1 ? A ILE 215 CG1 40 1 Y 1 A ILE 305 ? CG2 ? A ILE 215 CG2 41 1 Y 1 A ILE 305 ? CD1 ? A ILE 215 CD1 42 1 Y 1 A HIS 306 ? CG ? A HIS 216 CG 43 1 Y 1 A HIS 306 ? ND1 ? A HIS 216 ND1 44 1 Y 1 A HIS 306 ? CD2 ? A HIS 216 CD2 45 1 Y 1 A HIS 306 ? CE1 ? A HIS 216 CE1 46 1 Y 1 A HIS 306 ? NE2 ? A HIS 216 NE2 47 1 Y 1 A ASN 307 ? CG ? A ASN 217 CG 48 1 Y 1 A ASN 307 ? OD1 ? A ASN 217 OD1 49 1 Y 1 A ASN 307 ? ND2 ? A ASN 217 ND2 50 1 Y 1 A LEU 309 ? CG ? A LEU 219 CG 51 1 Y 1 A LEU 309 ? CD1 ? A LEU 219 CD1 52 1 Y 1 A LEU 309 ? CD2 ? A LEU 219 CD2 # _em_buffer_component.buffer_id 1 _em_buffer_component.id 1 _em_buffer_component.concentration 50 _em_buffer_component.concentration_units mM _em_buffer_component.formula NaPO4 _em_buffer_component.name 'Sodium Phosphate' # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.38 # _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 12844 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Sweet potato feathery mottle virus' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.ncbi_tax_id 4100 _em_entity_assembly_recombinant.organism 'Nicotiana benthamiana' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.angular_rotation_per_subunit 40.93 _em_helical_entity.axial_rise_per_subunit 3.98 _em_helical_entity.axial_symmetry C1 _em_helical_entity.details ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 1 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode COUNTING _em_image_recording.film_or_detector_model 'FEI FALCON III (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged 1 _em_image_recording.num_real_images 3276 _em_image_recording.avg_electron_dose_per_subtomogram ? # _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.details ? _em_particle_selection.method ? _em_particle_selection.num_particles_selected 313330 _em_particle_selection.reference_model ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 1 1 2 'IMAGE ACQUISITION' ? EPU ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? CTFFIND 4.1 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? 'UCSF Chimera' ? ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'MODEL REFINEMENT' ? PHENIX 1.19 ? 1 ? 10 'MODEL REFINEMENT' ? ISOLDE ? ? 1 ? 11 'MODEL REFINEMENT' ? Coot ? ? 1 ? 12 'INITIAL EULER ASSIGNMENT' ? RELION 3.1 1 ? ? 13 'FINAL EULER ASSIGNMENT' ? RELION 3.1 1 ? ? 14 CLASSIFICATION ? RELION 3.1 1 ? ? 15 RECONSTRUCTION ? RELION 3.1 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _em_virus_natural_host.id 1 _em_virus_natural_host.entity_assembly_id 1 _em_virus_natural_host.ncbi_tax_id 4120 _em_virus_natural_host.organism 'Ipomoea batatas' _em_virus_natural_host.strain ? # _em_virus_shell.id 1 _em_virus_shell.entity_assembly_id 1 _em_virus_shell.diameter 130 _em_virus_shell.name ? _em_virus_shell.triangulation ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Ministerio de Ciencia e Innovacion (MCIN)' Spain PID2019-105692RB-100 1 'Ministerio de Ciencia e Innovacion (MCIN)' Spain CEX2019-000902-S 2 'Biotechnology and Biological Sciences Research Council (BBSRC)' 'United Kingdom' BB/R001669/1 3 'Biotechnology and Biological Sciences Research Council (BBSRC)' 'United Kingdom' BB/T004703/1 4 # _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 ? # _space_group.crystal_system triclinic _space_group.name_H-M_alt 'P 1' _space_group.IT_number 1 _space_group.name_Hall 'P 1' _space_group.id 1 #