data_9VAM # _entry.id 9VAM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.414 _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 9VAM pdb_00009vam 10.2210/pdb9vam/pdb WWPDB D_1300060302 ? ? EMDB EMD-64901 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2026-06-10 ? 2 'EM metadata' 1 0 2026-06-10 ? 3 FSC 1 0 2026-06-10 ? 4 'Half map' 1 0 2026-06-10 1 5 'Half map' 1 0 2026-06-10 2 6 Image 1 0 2026-06-10 ? 7 'Primary map' 1 0 2026-06-10 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? 3 3 FSC repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 'Half map' repository 'Initial release' ? ? 6 6 Image repository 'Initial release' ? ? 7 7 'Primary map' repository 'Initial release' ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9VAM _pdbx_database_status.recvd_initial_deposition_date 2025-06-03 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBC _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 N # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of oat globulin fibril, Type 1' _pdbx_database_related.db_id EMD-64901 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email zhangyiling@sjtu.edu.cn _pdbx_contact_author.name_first Yiling _pdbx_contact_author.name_last Zhang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0009-0007-1927-3286 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Zhang, Y.L.' 1 ? 'Dai, B.' 2 ? # _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 structure of oat globulin fibril, Type 1' _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 'Zhang, Y.L.' 1 ? primary 'Dai, B.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description '12S seed storage globulin 2 basic chain' _entity.formula_weight 4055.648 _entity.pdbx_number_of_molecules 3 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'The protein that forms fibrils is 12S globulin, which is derived from oat.' # _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 VNLYQNAILSPYWNINAHSVMHMIQGRARVQVVNN _entity_poly.pdbx_seq_one_letter_code_can VNLYQNAILSPYWNINAHSVMHMIQGRARVQVVNN _entity_poly.pdbx_strand_id AC,AA,AB _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 VAL n 1 2 ASN n 1 3 LEU n 1 4 TYR n 1 5 GLN n 1 6 ASN n 1 7 ALA n 1 8 ILE n 1 9 LEU n 1 10 SER n 1 11 PRO n 1 12 TYR n 1 13 TRP n 1 14 ASN n 1 15 ILE n 1 16 ASN n 1 17 ALA n 1 18 HIS n 1 19 SER n 1 20 VAL n 1 21 MET n 1 22 HIS n 1 23 MET n 1 24 ILE n 1 25 GLN n 1 26 GLY n 1 27 ARG n 1 28 ALA n 1 29 ARG n 1 30 VAL n 1 31 GLN n 1 32 VAL n 1 33 VAL n 1 34 ASN n 1 35 ASN 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 oats _entity_src_nat.pdbx_organism_scientific 'Avena sativa' _entity_src_nat.pdbx_ncbi_taxonomy_id 4498 _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_ _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 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 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 VAL 1 369 369 VAL VAL AC . n A 1 2 ASN 2 370 370 ASN ASN AC . n A 1 3 LEU 3 371 371 LEU LEU AC . n A 1 4 TYR 4 372 372 TYR TYR AC . n A 1 5 GLN 5 373 373 GLN GLN AC . n A 1 6 ASN 6 374 374 ASN ASN AC . n A 1 7 ALA 7 375 375 ALA ALA AC . n A 1 8 ILE 8 376 376 ILE ILE AC . n A 1 9 LEU 9 377 377 LEU LEU AC . n A 1 10 SER 10 378 378 SER SER AC . n A 1 11 PRO 11 379 379 PRO PRO AC . n A 1 12 TYR 12 380 380 TYR TYR AC . n A 1 13 TRP 13 381 381 TRP TRP AC . n A 1 14 ASN 14 382 382 ASN ASN AC . n A 1 15 ILE 15 383 383 ILE ILE AC . n A 1 16 ASN 16 384 384 ASN ASN AC . n A 1 17 ALA 17 385 385 ALA ALA AC . n A 1 18 HIS 18 386 386 HIS HIS AC . n A 1 19 SER 19 387 387 SER SER AC . n A 1 20 VAL 20 388 388 VAL VAL AC . n A 1 21 MET 21 389 389 MET MET AC . n A 1 22 HIS 22 390 390 HIS HIS AC . n A 1 23 MET 23 391 391 MET MET AC . n A 1 24 ILE 24 392 392 ILE ILE AC . n A 1 25 GLN 25 393 393 GLN GLN AC . n A 1 26 GLY 26 394 394 GLY GLY AC . n A 1 27 ARG 27 395 395 ARG ARG AC . n A 1 28 ALA 28 396 396 ALA ALA AC . n A 1 29 ARG 29 397 397 ARG ARG AC . n A 1 30 VAL 30 398 398 VAL VAL AC . n A 1 31 GLN 31 399 399 GLN GLN AC . n A 1 32 VAL 32 400 400 VAL VAL AC . n A 1 33 VAL 33 401 401 VAL VAL AC . n A 1 34 ASN 34 402 402 ASN ASN AC . n A 1 35 ASN 35 403 403 ASN ASN AC . n B 1 1 VAL 1 369 369 VAL VAL AA . n B 1 2 ASN 2 370 370 ASN ASN AA . n B 1 3 LEU 3 371 371 LEU LEU AA . n B 1 4 TYR 4 372 372 TYR TYR AA . n B 1 5 GLN 5 373 373 GLN GLN AA . n B 1 6 ASN 6 374 374 ASN ASN AA . n B 1 7 ALA 7 375 375 ALA ALA AA . n B 1 8 ILE 8 376 376 ILE ILE AA . n B 1 9 LEU 9 377 377 LEU LEU AA . n B 1 10 SER 10 378 378 SER SER AA . n B 1 11 PRO 11 379 379 PRO PRO AA . n B 1 12 TYR 12 380 380 TYR TYR AA . n B 1 13 TRP 13 381 381 TRP TRP AA . n B 1 14 ASN 14 382 382 ASN ASN AA . n B 1 15 ILE 15 383 383 ILE ILE AA . n B 1 16 ASN 16 384 384 ASN ASN AA . n B 1 17 ALA 17 385 385 ALA ALA AA . n B 1 18 HIS 18 386 386 HIS HIS AA . n B 1 19 SER 19 387 387 SER SER AA . n B 1 20 VAL 20 388 388 VAL VAL AA . n B 1 21 MET 21 389 389 MET MET AA . n B 1 22 HIS 22 390 390 HIS HIS AA . n B 1 23 MET 23 391 391 MET MET AA . n B 1 24 ILE 24 392 392 ILE ILE AA . n B 1 25 GLN 25 393 393 GLN GLN AA . n B 1 26 GLY 26 394 394 GLY GLY AA . n B 1 27 ARG 27 395 395 ARG ARG AA . n B 1 28 ALA 28 396 396 ALA ALA AA . n B 1 29 ARG 29 397 397 ARG ARG AA . n B 1 30 VAL 30 398 398 VAL VAL AA . n B 1 31 GLN 31 399 399 GLN GLN AA . n B 1 32 VAL 32 400 400 VAL VAL AA . n B 1 33 VAL 33 401 401 VAL VAL AA . n B 1 34 ASN 34 402 402 ASN ASN AA . n B 1 35 ASN 35 403 403 ASN ASN AA . n C 1 1 VAL 1 369 369 VAL VAL AB . n C 1 2 ASN 2 370 370 ASN ASN AB . n C 1 3 LEU 3 371 371 LEU LEU AB . n C 1 4 TYR 4 372 372 TYR TYR AB . n C 1 5 GLN 5 373 373 GLN GLN AB . n C 1 6 ASN 6 374 374 ASN ASN AB . n C 1 7 ALA 7 375 375 ALA ALA AB . n C 1 8 ILE 8 376 376 ILE ILE AB . n C 1 9 LEU 9 377 377 LEU LEU AB . n C 1 10 SER 10 378 378 SER SER AB . n C 1 11 PRO 11 379 379 PRO PRO AB . n C 1 12 TYR 12 380 380 TYR TYR AB . n C 1 13 TRP 13 381 381 TRP TRP AB . n C 1 14 ASN 14 382 382 ASN ASN AB . n C 1 15 ILE 15 383 383 ILE ILE AB . n C 1 16 ASN 16 384 384 ASN ASN AB . n C 1 17 ALA 17 385 385 ALA ALA AB . n C 1 18 HIS 18 386 386 HIS HIS AB . n C 1 19 SER 19 387 387 SER SER AB . n C 1 20 VAL 20 388 388 VAL VAL AB . n C 1 21 MET 21 389 389 MET MET AB . n C 1 22 HIS 22 390 390 HIS HIS AB . n C 1 23 MET 23 391 391 MET MET AB . n C 1 24 ILE 24 392 392 ILE ILE AB . n C 1 25 GLN 25 393 393 GLN GLN AB . n C 1 26 GLY 26 394 394 GLY GLY AB . n C 1 27 ARG 27 395 395 ARG ARG AB . n C 1 28 ALA 28 396 396 ALA ALA AB . n C 1 29 ARG 29 397 397 ARG ARG AB . n C 1 30 VAL 30 398 398 VAL VAL AB . n C 1 31 GLN 31 399 399 GLN GLN AB . n C 1 32 VAL 32 400 400 VAL VAL AB . n C 1 33 VAL 33 401 401 VAL VAL AB . n C 1 34 ASN 34 402 402 ASN ASN AB . n C 1 35 ASN 35 403 403 ASN ASN AB . 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 9VAM _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 9VAM _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 9VAM _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 ? _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 9VAM _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.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _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 ? _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_Zscore _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.0052 ? 870 ? f_bond_d ? ? ? 'ELECTRON MICROSCOPY' ? 0.9523 ? 1185 ? f_angle_d ? ? ? 'ELECTRON MICROSCOPY' ? 0.0751 ? 132 ? f_chiral_restr ? ? ? 'ELECTRON MICROSCOPY' ? 0.0101 ? 153 ? f_plane_restr ? ? ? 'ELECTRON MICROSCOPY' ? 18.3401 ? 513 ? f_dihedral_angle_d ? ? ? # _struct.entry_id 9VAM _struct.title 'Cryo-EM structure of oat globulin fibril, Type 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 9VAM _struct_keywords.text 'PROTEIN FIBRIL, amyloid, oat globulin' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # 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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SSG2_AVESA _struct_ref.pdbx_db_accession P14812 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code VNLYQNAILSPYWNINAHSVMHMIQGRARVQVVNN _struct_ref.pdbx_align_begin 369 # 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 9VAM AC 1 ? 35 ? P14812 369 ? 403 ? 369 403 2 1 9VAM AA 1 ? 35 ? P14812 369 ? 403 ? 369 403 3 1 9VAM AB 1 ? 35 ? P14812 369 ? 403 ? 369 403 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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 x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 3 ? AA3 ? 3 ? # 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 AA2 1 2 ? parallel AA2 2 3 ? parallel AA3 1 2 ? parallel AA3 2 3 ? 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 ILE A 15 ? ASN A 16 ? ILE AC 383 ASN AC 384 AA1 2 ILE B 15 ? ASN B 16 ? ILE AA 383 ASN AA 384 AA1 3 ILE C 15 ? ASN C 16 ? ILE AB 383 ASN AB 384 AA2 1 MET A 21 ? ILE A 24 ? MET AC 389 ILE AC 392 AA2 2 MET B 21 ? ILE B 24 ? MET AA 389 ILE AA 392 AA2 3 MET C 21 ? ILE C 24 ? MET AB 389 ILE AB 392 AA3 1 ARG A 27 ? VAL A 33 ? ARG AC 395 VAL AC 401 AA3 2 ARG B 27 ? VAL B 33 ? ARG AA 395 VAL AA 401 AA3 3 ARG C 27 ? VAL C 33 ? ARG AB 395 VAL AB 401 # 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 ASN A 16 ? N ASN AC 384 O ILE B 15 ? O ILE AA 383 AA1 2 3 N ASN B 16 ? N ASN AA 384 O ILE C 15 ? O ILE AB 383 AA2 1 2 N MET A 23 ? N MET AC 391 O HIS B 22 ? O HIS AA 390 AA2 2 3 N MET B 23 ? N MET AA 391 O HIS C 22 ? O HIS AB 390 AA3 1 2 N ARG A 29 ? N ARG AC 397 O VAL B 30 ? O VAL AA 398 AA3 2 3 N ARG B 29 ? N ARG AA 397 O VAL C 30 ? O VAL AB 398 # _pdbx_entry_details.entry_id 9VAM _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 # 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 TYR AC 372 ? ? -161.10 116.54 2 1 ALA AC 375 ? ? 176.96 -179.64 3 1 TYR AA 372 ? ? -161.10 116.54 4 1 ALA AA 375 ? ? 176.96 -179.64 5 1 TYR AB 372 ? ? -161.10 116.54 6 1 ALA AB 375 ? ? 176.96 -179.64 # _space_group_symop.id 1 _space_group_symop.operation_xyz x,y,z # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9VAM _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 9VAM _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 3.88 _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 22559 _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 HELICAL # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 2 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type TISSUE _em_entity_assembly.name 'Cryo-EM structure of oat globulin fibril, Type 1' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9VAM _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'TFS KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 1000 _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 ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? _em_imaging.objective_aperture ? _em_imaging.microscope_serial_number ? _em_imaging.microscope_version ? # _em_vitrification.entry_id 9VAM _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9VAM _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _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 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 GLN N N N N 58 GLN CA C N S 59 GLN C C N N 60 GLN O O N N 61 GLN CB C N N 62 GLN CG C N N 63 GLN CD C N N 64 GLN OE1 O N N 65 GLN NE2 N N N 66 GLN OXT O N N 67 GLN H H N N 68 GLN H2 H N N 69 GLN HA H N N 70 GLN HB2 H N N 71 GLN HB3 H N N 72 GLN HG2 H N N 73 GLN HG3 H N N 74 GLN HE21 H N N 75 GLN HE22 H N N 76 GLN HXT H N N 77 GLY N N N N 78 GLY CA C N N 79 GLY C C N N 80 GLY O O N N 81 GLY OXT O N N 82 GLY H H N N 83 GLY H2 H N N 84 GLY HA2 H N N 85 GLY HA3 H N N 86 GLY HXT H N N 87 HIS N N N N 88 HIS CA C N S 89 HIS C C N N 90 HIS O O N N 91 HIS CB C N N 92 HIS CG C Y N 93 HIS ND1 N Y N 94 HIS CD2 C Y N 95 HIS CE1 C Y N 96 HIS NE2 N Y N 97 HIS OXT O N N 98 HIS H H N N 99 HIS H2 H N N 100 HIS HA H N N 101 HIS HB2 H N N 102 HIS HB3 H N N 103 HIS HD1 H N N 104 HIS HD2 H N N 105 HIS HE1 H N N 106 HIS HE2 H N N 107 HIS HXT H N N 108 ILE N N N N 109 ILE CA C N S 110 ILE C C N N 111 ILE O O N N 112 ILE CB C N S 113 ILE CG1 C N N 114 ILE CG2 C N N 115 ILE CD1 C N N 116 ILE OXT O N N 117 ILE H H N N 118 ILE H2 H N N 119 ILE HA H N N 120 ILE HB H N N 121 ILE HG12 H N N 122 ILE HG13 H N N 123 ILE HG21 H N N 124 ILE HG22 H N N 125 ILE HG23 H N N 126 ILE HD11 H N N 127 ILE HD12 H N N 128 ILE HD13 H N N 129 ILE HXT H N N 130 LEU N N N N 131 LEU CA C N S 132 LEU C C N N 133 LEU O O N N 134 LEU CB C N N 135 LEU CG C N N 136 LEU CD1 C N N 137 LEU CD2 C N N 138 LEU OXT O N N 139 LEU H H N N 140 LEU H2 H N N 141 LEU HA H N N 142 LEU HB2 H N N 143 LEU HB3 H N N 144 LEU HG H N N 145 LEU HD11 H N N 146 LEU HD12 H N N 147 LEU HD13 H N N 148 LEU HD21 H N N 149 LEU HD22 H N N 150 LEU HD23 H N N 151 LEU HXT H N N 152 MET N N N N 153 MET CA C N S 154 MET C C N N 155 MET O O N N 156 MET CB C N N 157 MET CG C N N 158 MET SD S N N 159 MET CE C N N 160 MET OXT O N N 161 MET H H N N 162 MET H2 H N N 163 MET HA H N N 164 MET HB2 H N N 165 MET HB3 H N N 166 MET HG2 H N N 167 MET HG3 H N N 168 MET HE1 H N N 169 MET HE2 H N N 170 MET HE3 H N N 171 MET HXT H N N 172 PRO N N N N 173 PRO CA C N S 174 PRO C C N N 175 PRO O O N N 176 PRO CB C N N 177 PRO CG C N N 178 PRO CD C N N 179 PRO OXT O N N 180 PRO H H N N 181 PRO HA H N N 182 PRO HB2 H N N 183 PRO HB3 H N N 184 PRO HG2 H N N 185 PRO HG3 H N N 186 PRO HD2 H N N 187 PRO HD3 H N N 188 PRO HXT H N N 189 SER N N N N 190 SER CA C N S 191 SER C C N N 192 SER O O N N 193 SER CB C N N 194 SER OG O N N 195 SER OXT O N N 196 SER H H N N 197 SER H2 H N N 198 SER HA H N N 199 SER HB2 H N N 200 SER HB3 H N N 201 SER HG H N N 202 SER HXT H N N 203 TRP N N N N 204 TRP CA C N S 205 TRP C C N N 206 TRP O O N N 207 TRP CB C N N 208 TRP CG C Y N 209 TRP CD1 C Y N 210 TRP CD2 C Y N 211 TRP NE1 N Y N 212 TRP CE2 C Y N 213 TRP CE3 C Y N 214 TRP CZ2 C Y N 215 TRP CZ3 C Y N 216 TRP CH2 C Y N 217 TRP OXT O N N 218 TRP H H N N 219 TRP H2 H N N 220 TRP HA H N N 221 TRP HB2 H N N 222 TRP HB3 H N N 223 TRP HD1 H N N 224 TRP HE1 H N N 225 TRP HE3 H N N 226 TRP HZ2 H N N 227 TRP HZ3 H N N 228 TRP HH2 H N N 229 TRP HXT H N N 230 TYR N N N N 231 TYR CA C N S 232 TYR C C N N 233 TYR O O N N 234 TYR CB C N N 235 TYR CG C Y N 236 TYR CD1 C Y N 237 TYR CD2 C Y N 238 TYR CE1 C Y N 239 TYR CE2 C Y N 240 TYR CZ C Y N 241 TYR OH O N N 242 TYR OXT O N N 243 TYR H H N N 244 TYR H2 H N N 245 TYR HA H N N 246 TYR HB2 H N N 247 TYR HB3 H N N 248 TYR HD1 H N N 249 TYR HD2 H N N 250 TYR HE1 H N N 251 TYR HE2 H N N 252 TYR HH H N N 253 TYR HXT H N N 254 VAL N N N N 255 VAL CA C N S 256 VAL C C N N 257 VAL O O N N 258 VAL CB C N N 259 VAL CG1 C N N 260 VAL CG2 C N N 261 VAL OXT O N N 262 VAL H H N N 263 VAL H2 H N N 264 VAL HA H N N 265 VAL HB H N N 266 VAL HG11 H N N 267 VAL HG12 H N N 268 VAL HG13 H N N 269 VAL HG21 H N N 270 VAL HG22 H N N 271 VAL HG23 H N N 272 VAL HXT H N N 273 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 GLN N CA sing N N 55 GLN N H sing N N 56 GLN N H2 sing N N 57 GLN CA C sing N N 58 GLN CA CB sing N N 59 GLN CA HA sing N N 60 GLN C O doub N N 61 GLN C OXT sing N N 62 GLN CB CG sing N N 63 GLN CB HB2 sing N N 64 GLN CB HB3 sing N N 65 GLN CG CD sing N N 66 GLN CG HG2 sing N N 67 GLN CG HG3 sing N N 68 GLN CD OE1 doub N N 69 GLN CD NE2 sing N N 70 GLN NE2 HE21 sing N N 71 GLN NE2 HE22 sing N N 72 GLN OXT HXT sing N N 73 GLY N CA sing N N 74 GLY N H sing N N 75 GLY N H2 sing N N 76 GLY CA C sing N N 77 GLY CA HA2 sing N N 78 GLY CA HA3 sing N N 79 GLY C O doub N N 80 GLY C OXT sing N N 81 GLY OXT HXT sing N N 82 HIS N CA sing N N 83 HIS N H sing N N 84 HIS N H2 sing N N 85 HIS CA C sing N N 86 HIS CA CB sing N N 87 HIS CA HA sing N N 88 HIS C O doub N N 89 HIS C OXT sing N N 90 HIS CB CG sing N N 91 HIS CB HB2 sing N N 92 HIS CB HB3 sing N N 93 HIS CG ND1 sing Y N 94 HIS CG CD2 doub Y N 95 HIS ND1 CE1 doub Y N 96 HIS ND1 HD1 sing N N 97 HIS CD2 NE2 sing Y N 98 HIS CD2 HD2 sing N N 99 HIS CE1 NE2 sing Y N 100 HIS CE1 HE1 sing N N 101 HIS NE2 HE2 sing N N 102 HIS OXT HXT sing N N 103 ILE N CA sing N N 104 ILE N H sing N N 105 ILE N H2 sing N N 106 ILE CA C sing N N 107 ILE CA CB sing N N 108 ILE CA HA sing N N 109 ILE C O doub N N 110 ILE C OXT sing N N 111 ILE CB CG1 sing N N 112 ILE CB CG2 sing N N 113 ILE CB HB sing N N 114 ILE CG1 CD1 sing N N 115 ILE CG1 HG12 sing N N 116 ILE CG1 HG13 sing N N 117 ILE CG2 HG21 sing N N 118 ILE CG2 HG22 sing N N 119 ILE CG2 HG23 sing N N 120 ILE CD1 HD11 sing N N 121 ILE CD1 HD12 sing N N 122 ILE CD1 HD13 sing N N 123 ILE OXT HXT sing N N 124 LEU N CA sing N N 125 LEU N H sing N N 126 LEU N H2 sing N N 127 LEU CA C sing N N 128 LEU CA CB sing N N 129 LEU CA HA sing N N 130 LEU C O doub N N 131 LEU C OXT sing N N 132 LEU CB CG sing N N 133 LEU CB HB2 sing N N 134 LEU CB HB3 sing N N 135 LEU CG CD1 sing N N 136 LEU CG CD2 sing N N 137 LEU CG HG sing N N 138 LEU CD1 HD11 sing N N 139 LEU CD1 HD12 sing N N 140 LEU CD1 HD13 sing N N 141 LEU CD2 HD21 sing N N 142 LEU CD2 HD22 sing N N 143 LEU CD2 HD23 sing N N 144 LEU OXT HXT sing N N 145 MET N CA sing N N 146 MET N H sing N N 147 MET N H2 sing N N 148 MET CA C sing N N 149 MET CA CB sing N N 150 MET CA HA sing N N 151 MET C O doub N N 152 MET C OXT sing N N 153 MET CB CG sing N N 154 MET CB HB2 sing N N 155 MET CB HB3 sing N N 156 MET CG SD sing N N 157 MET CG HG2 sing N N 158 MET CG HG3 sing N N 159 MET SD CE sing N N 160 MET CE HE1 sing N N 161 MET CE HE2 sing N N 162 MET CE HE3 sing N N 163 MET OXT HXT sing N N 164 PRO N CA sing N N 165 PRO N CD sing N N 166 PRO N H sing N N 167 PRO CA C sing N N 168 PRO CA CB sing N N 169 PRO CA HA sing N N 170 PRO C O doub N N 171 PRO C OXT sing N N 172 PRO CB CG sing N N 173 PRO CB HB2 sing N N 174 PRO CB HB3 sing N N 175 PRO CG CD sing N N 176 PRO CG HG2 sing N N 177 PRO CG HG3 sing N N 178 PRO CD HD2 sing N N 179 PRO CD HD3 sing N N 180 PRO OXT HXT sing N N 181 SER N CA sing N N 182 SER N H sing N N 183 SER N H2 sing N N 184 SER CA C sing N N 185 SER CA CB sing N N 186 SER CA HA sing N N 187 SER C O doub N N 188 SER C OXT sing N N 189 SER CB OG sing N N 190 SER CB HB2 sing N N 191 SER CB HB3 sing N N 192 SER OG HG sing N N 193 SER OXT HXT sing N N 194 TRP N CA sing N N 195 TRP N H sing N N 196 TRP N H2 sing N N 197 TRP CA C sing N N 198 TRP CA CB sing N N 199 TRP CA HA sing N N 200 TRP C O doub N N 201 TRP C OXT sing N N 202 TRP CB CG sing N N 203 TRP CB HB2 sing N N 204 TRP CB HB3 sing N N 205 TRP CG CD1 doub Y N 206 TRP CG CD2 sing Y N 207 TRP CD1 NE1 sing Y N 208 TRP CD1 HD1 sing N N 209 TRP CD2 CE2 doub Y N 210 TRP CD2 CE3 sing Y N 211 TRP NE1 CE2 sing Y N 212 TRP NE1 HE1 sing N N 213 TRP CE2 CZ2 sing Y N 214 TRP CE3 CZ3 doub Y N 215 TRP CE3 HE3 sing N N 216 TRP CZ2 CH2 doub Y N 217 TRP CZ2 HZ2 sing N N 218 TRP CZ3 CH2 sing Y N 219 TRP CZ3 HZ3 sing N N 220 TRP CH2 HH2 sing N N 221 TRP OXT HXT sing N N 222 TYR N CA sing N N 223 TYR N H sing N N 224 TYR N H2 sing N N 225 TYR CA C sing N N 226 TYR CA CB sing N N 227 TYR CA HA sing N N 228 TYR C O doub N N 229 TYR C OXT sing N N 230 TYR CB CG sing N N 231 TYR CB HB2 sing N N 232 TYR CB HB3 sing N N 233 TYR CG CD1 doub Y N 234 TYR CG CD2 sing Y N 235 TYR CD1 CE1 sing Y N 236 TYR CD1 HD1 sing N N 237 TYR CD2 CE2 doub Y N 238 TYR CD2 HD2 sing N N 239 TYR CE1 CZ doub Y N 240 TYR CE1 HE1 sing N N 241 TYR CE2 CZ sing Y N 242 TYR CE2 HE2 sing N N 243 TYR CZ OH sing N N 244 TYR OH HH sing N N 245 TYR OXT HXT sing N N 246 VAL N CA sing N N 247 VAL N H sing N N 248 VAL N H2 sing N N 249 VAL CA C sing N N 250 VAL CA CB sing N N 251 VAL CA HA sing N N 252 VAL C O doub N N 253 VAL C OXT sing N N 254 VAL CB CG1 sing N N 255 VAL CB CG2 sing N N 256 VAL CB HB sing N N 257 VAL CG1 HG11 sing N N 258 VAL CG1 HG12 sing N N 259 VAL CG1 HG13 sing N N 260 VAL CG2 HG21 sing N N 261 VAL CG2 HG22 sing N N 262 VAL CG2 HG23 sing N N 263 VAL OXT HXT sing N N 264 # _em_admin.current_status REL _em_admin.deposition_date 2025-06-03 _em_admin.deposition_site PDBJ _em_admin.entry_id 9VAM _em_admin.last_update 2026-06-10 _em_admin.map_release_date 2026-06-10 _em_admin.title 'Cryo-EM structure of oat globulin fibril, Type 1' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type NONE # _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 50455 _em_entity_assembly_naturalsource.organism 'Avena sp.' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.details ? _em_helical_entity.axial_symmetry C1 _em_helical_entity.angular_rotation_per_subunit -1.58 _em_helical_entity.axial_rise_per_subunit 4.8 # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 55 _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 ? # 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 _em_software.reference_DOI 'PARTICLE SELECTION' ? 1 1 ? ? RELION ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? ? MASKING ? 3 ? ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? ? ? ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? ? ? ? OTHER ? 8 ? ? ? ? ? ? 'MODEL REFINEMENT' ? 9 ? 1 ? PHENIX 1.15.2_3472 ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? ? RECONSTRUCTION ? 13 1 ? ? RELION ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Not funded' _pdbx_audit_support.country ? _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _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 # _atom_sites.entry_id 9VAM _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_ #