data_7VI4 # _entry.id 7VI4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.360 _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 7VI4 pdb_00007vi4 10.2210/pdb7vi4/pdb WWPDB D_1300024729 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7VI4 _pdbx_database_status.recvd_initial_deposition_date 2021-09-24 _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 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Takaba, K.' 1 ? 'Maki-Yonekura, S.' 2 ? 'Sekiyama, N.' 3 ? 'Imamura, K.' 4 ? 'Kodama, T.' 5 ? 'Tochio, H.' 6 ? 'Yonekura, K.' 7 ? # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_id_ASTM PNASA6 _citation.journal_id_CSD 0040 _citation.journal_id_ISSN 1091-6490 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 119 _citation.language ? _citation.page_first e2122523119 _citation.page_last e2122523119 _citation.title 'ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1073/pnas.2122523119 _citation.pdbx_database_id_PubMed 36112647 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sekiyama, N.' 1 0000-0003-4537-6565 primary 'Takaba, K.' 2 ? primary 'Maki-Yonekura, S.' 3 ? primary 'Akagi, K.I.' 4 0000-0002-7051-4598 primary 'Ohtani, Y.' 5 ? primary 'Imamura, K.' 6 0000-0002-2141-8495 primary 'Terakawa, T.' 7 ? primary 'Yamashita, K.' 8 ? primary 'Inaoka, D.' 9 0000-0002-8643-4031 primary 'Yonekura, K.' 10 0000-0001-5520-4391 primary 'Kodama, T.S.' 11 0000-0001-6820-1907 primary 'Tochio, H.' 12 0000-0003-3843-3330 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 116.150 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 7VI4 _cell.details ? _cell.formula_units_Z ? _cell.length_a 30.680 _cell.length_a_esd ? _cell.length_b 9.630 _cell.length_b_esd ? _cell.length_c 26.250 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _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 ? # _symmetry.entry_id 7VI4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 syn 'TIA-1 prion-like domain' 1174.241 1 ? A381T ? ? 2 water nat water 18.015 3 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'RNA-binding protein TIA-1,T-cell-restricted intracellular antigen-1,TIA-1,p40-TIA-1' # _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 GYRVTGYETQ _entity_poly.pdbx_seq_one_letter_code_can GYRVTGYETQ _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 TYR n 1 3 ARG n 1 4 VAL n 1 5 THR n 1 6 GLY n 1 7 TYR n 1 8 GLU n 1 9 THR n 1 10 GLN n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name Human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TIA1_HUMAN _struct_ref.pdbx_db_accession P31483 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GYRVAGYETQ _struct_ref.pdbx_align_begin 377 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7VI4 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P31483 _struct_ref_seq.db_align_beg 377 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 386 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 7VI4 _struct_ref_seq_dif.mon_id THR _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 5 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code P31483 _struct_ref_seq_dif.db_mon_id ALA _struct_ref_seq_dif.pdbx_seq_db_seq_num 381 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 5 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 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 7VI4 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON CRYSTALLOGRAPHY' _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 31.270 _refine.B_iso_mean 6.7458 _refine.B_iso_min 0.560 _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 7VI4 _refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _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 0.9500 _refine.ls_d_res_low 15.1470 _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 3537 _refine.ls_number_reflns_R_free 356 _refine.ls_number_reflns_R_work 3181 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 77.5700 _refine.ls_percent_reflns_R_free 10.0700 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2558 _refine.ls_R_factor_R_free 0.3073 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2491 _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 'FLAT BULK SOLVENT MODEL' _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 1.350 _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 THROUGHOUT _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _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 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _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 34.6600 _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 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.1600 _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 ? # _refine_hist.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 0.9500 _refine_hist.d_res_low 15.1470 _refine_hist.number_atoms_solvent 4 _refine_hist.number_atoms_total 87 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 10 _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent 8.28 _refine_hist.pdbx_number_atoms_protein 83 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # 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 CRYSTALLOGRAPHY' ? 0.059 ? 84 ? f_bond_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 3.442 ? 113 ? f_angle_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.172 ? 11 ? f_chiral_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.052 ? 15 ? f_plane_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 34.424 ? 30 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'ELECTRON CRYSTALLOGRAPHY' 0.9502 1.0876 . . 116 1036 77.0000 . . . 0.3778 0.0000 0.2993 . . . . . . . . . . . 'ELECTRON CRYSTALLOGRAPHY' 1.0876 1.3701 . . 119 1057 78.0000 . . . 0.2757 0.0000 0.2511 . . . . . . . . . . . 'ELECTRON CRYSTALLOGRAPHY' 1.3701 15.1470 . . 121 1088 77.0000 . . . 0.2947 0.0000 0.2252 . . . . . . . . . . . # _struct.entry_id 7VI4 _struct.title 'Electron crystallographic structure of TIA-1 prion-like domain, A381T mutant' _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 7VI4 _struct_keywords.text 'ALS, prion, fibril, PROTEIN FIBRIL' _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 2 ? # _atom_sites.entry_id 7VI4 _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] 0.032595 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.016003 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.103842 _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] 0.042439 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . GLY A 1 1 ? -6.177 4.105 -9.216 1.00 6.53 ? 1 GLY A N 1 ATOM 2 C CA . GLY A 1 1 ? -4.975 3.472 -8.657 1.00 2.18 ? 1 GLY A CA 1 ATOM 3 C C . GLY A 1 1 ? -4.059 4.469 -8.002 1.00 3.02 ? 1 GLY A C 1 ATOM 4 O O . GLY A 1 1 ? -4.256 5.679 -7.943 1.00 6.20 ? 1 GLY A O 1 ATOM 5 N N . TYR A 1 2 ? -2.957 3.915 -7.442 1.00 3.76 ? 2 TYR A N 1 ATOM 6 C CA . TYR A 1 2 ? -1.971 4.757 -6.767 1.00 3.29 ? 2 TYR A CA 1 ATOM 7 C C . TYR A 1 2 ? -0.694 3.928 -6.539 1.00 2.25 ? 2 TYR A C 1 ATOM 8 O O . TYR A 1 2 ? -0.742 2.701 -6.695 1.00 4.73 ? 2 TYR A O 1 ATOM 9 C CB . TYR A 1 2 ? -2.507 5.344 -5.471 1.00 3.58 ? 2 TYR A CB 1 ATOM 10 C CG . TYR A 1 2 ? -3.083 4.373 -4.491 1.00 4.86 ? 2 TYR A CG 1 ATOM 11 C CD1 . TYR A 1 2 ? -2.266 3.696 -3.566 1.00 4.74 ? 2 TYR A CD1 1 ATOM 12 C CD2 . TYR A 1 2 ? -4.429 4.085 -4.437 1.00 4.27 ? 2 TYR A CD2 1 ATOM 13 C CE1 . TYR A 1 2 ? -2.816 2.797 -2.671 1.00 9.05 ? 2 TYR A CE1 1 ATOM 14 C CE2 . TYR A 1 2 ? -4.998 3.199 -3.550 1.00 6.35 ? 2 TYR A CE2 1 ATOM 15 C CZ . TYR A 1 2 ? -4.166 2.558 -2.661 1.00 6.93 ? 2 TYR A CZ 1 ATOM 16 O OH . TYR A 1 2 ? -4.725 1.667 -1.767 1.00 17.71 ? 2 TYR A OH 1 ATOM 17 N N . ARG A 1 3 ? 0.368 4.598 -6.236 1.00 1.91 ? 3 ARG A N 1 ATOM 18 C CA . ARG A 1 3 ? 1.701 4.067 -5.961 1.00 3.70 ? 3 ARG A CA 1 ATOM 19 C C . ARG A 1 3 ? 2.214 4.709 -4.665 1.00 0.79 ? 3 ARG A C 1 ATOM 20 O O . ARG A 1 3 ? 1.994 5.873 -4.438 1.00 4.06 ? 3 ARG A O 1 ATOM 21 C CB . ARG A 1 3 ? 2.681 4.340 -7.092 1.00 2.98 ? 3 ARG A CB 1 ATOM 22 C CG . ARG A 1 3 ? 2.208 3.873 -8.449 1.00 6.90 ? 3 ARG A CG 1 ATOM 23 C CD . ARG A 1 3 ? 3.145 4.066 -9.600 1.00 8.04 ? 3 ARG A CD 1 ATOM 24 N NE . ARG A 1 3 ? 4.559 4.119 -9.337 1.00 31.27 ? 3 ARG A NE 1 ATOM 25 C CZ . ARG A 1 3 ? 5.592 4.703 -9.918 1.00 7.91 ? 3 ARG A CZ 1 ATOM 26 N NH1 . ARG A 1 3 ? 5.726 6.001 -10.142 1.00 14.16 ? 3 ARG A NH1 1 ATOM 27 N NH2 . ARG A 1 3 ? 6.606 3.907 -10.244 1.00 12.64 ? 3 ARG A NH2 1 ATOM 28 N N . VAL A 1 4 ? 2.906 3.884 -3.905 1.00 4.26 ? 4 VAL A N 1 ATOM 29 C CA . VAL A 1 4 ? 3.580 4.387 -2.691 1.00 3.22 ? 4 VAL A CA 1 ATOM 30 C C . VAL A 1 4 ? 4.864 3.664 -2.388 1.00 1.50 ? 4 VAL A C 1 ATOM 31 O O . VAL A 1 4 ? 4.978 2.456 -2.585 1.00 4.21 ? 4 VAL A O 1 ATOM 32 C CB . VAL A 1 4 ? 2.610 4.341 -1.505 1.00 6.60 ? 4 VAL A CB 1 ATOM 33 C CG1 . VAL A 1 4 ? 2.125 2.928 -1.233 1.00 12.76 ? 4 VAL A CG1 1 ATOM 34 C CG2 . VAL A 1 4 ? 3.255 4.922 -0.250 1.00 10.02 ? 4 VAL A CG2 1 ATOM 35 N N . THR A 1 5 ? 5.832 4.391 -1.908 1.00 3.34 ? 5 THR A N 1 ATOM 36 C CA . THR A 1 5 ? 7.115 3.853 -1.460 1.00 2.68 ? 5 THR A CA 1 ATOM 37 C C . THR A 1 5 ? 7.497 4.506 -0.133 1.00 0.56 ? 5 THR A C 1 ATOM 38 O O . THR A 1 5 ? 7.164 5.679 0.073 1.00 5.73 ? 5 THR A O 1 ATOM 39 C CB . THR A 1 5 ? 8.243 3.999 -2.477 1.00 5.22 ? 5 THR A CB 1 ATOM 40 O OG1 . THR A 1 5 ? 8.427 5.390 -2.811 1.00 16.05 ? 5 THR A OG1 1 ATOM 41 C CG2 . THR A 1 5 ? 7.992 3.289 -3.803 1.00 7.58 ? 5 THR A CG2 1 ATOM 42 N N . GLY A 1 6 ? 8.161 3.869 0.737 1.00 3.90 ? 6 GLY A N 1 ATOM 43 C CA . GLY A 1 6 ? 9.001 4.479 1.757 1.00 2.90 ? 6 GLY A CA 1 ATOM 44 C C . GLY A 1 6 ? 10.252 3.715 2.065 1.00 3.32 ? 6 GLY A C 1 ATOM 45 O O . GLY A 1 6 ? 10.368 2.515 1.913 1.00 6.84 ? 6 GLY A O 1 ATOM 46 N N . TYR A 1 7 ? 11.265 4.464 2.616 1.00 2.55 ? 7 TYR A N 1 ATOM 47 C CA . TYR A 1 7 ? 12.593 3.935 2.841 1.00 4.22 ? 7 TYR A CA 1 ATOM 48 C C . TYR A 1 7 ? 13.148 4.692 4.065 1.00 0.95 ? 7 TYR A C 1 ATOM 49 O O . TYR A 1 7 ? 12.984 5.906 4.104 1.00 4.73 ? 7 TYR A O 1 ATOM 50 C CB . TYR A 1 7 ? 13.557 4.116 1.681 0.70 2.34 ? 7 TYR A CB 1 ATOM 51 C CG . TYR A 1 7 ? 14.991 3.817 2.105 0.70 2.47 ? 7 TYR A CG 1 ATOM 52 C CD1 . TYR A 1 7 ? 15.528 2.551 1.962 0.70 6.99 ? 7 TYR A CD1 1 ATOM 53 C CD2 . TYR A 1 7 ? 15.820 4.775 2.670 0.70 3.89 ? 7 TYR A CD2 1 ATOM 54 C CE1 . TYR A 1 7 ? 16.822 2.252 2.345 0.70 10.81 ? 7 TYR A CE1 1 ATOM 55 C CE2 . TYR A 1 7 ? 17.125 4.497 3.065 0.70 8.34 ? 7 TYR A CE2 1 ATOM 56 C CZ . TYR A 1 7 ? 17.623 3.215 2.900 0.70 6.51 ? 7 TYR A CZ 1 ATOM 57 O OH . TYR A 1 7 ? 18.910 2.940 3.281 0.70 22.89 ? 7 TYR A OH 1 ATOM 58 N N . GLU A 1 8 ? 13.753 3.975 5.006 1.00 4.41 ? 8 GLU A N 1 ATOM 59 C CA . GLU A 1 8 ? 14.496 4.684 6.041 1.00 1.35 ? 8 GLU A CA 1 ATOM 60 C C . GLU A 1 8 ? 15.685 3.857 6.524 1.00 2.77 ? 8 GLU A C 1 ATOM 61 O O . GLU A 1 8 ? 15.644 2.660 6.475 1.00 4.22 ? 8 GLU A O 1 ATOM 62 C CB . GLU A 1 8 ? 13.556 4.943 7.206 1.00 4.85 ? 8 GLU A CB 1 ATOM 63 C CG . GLU A 1 8 ? 13.043 3.703 7.888 1.00 5.12 ? 8 GLU A CG 1 ATOM 64 C CD . GLU A 1 8 ? 12.225 3.985 9.119 1.00 8.18 ? 8 GLU A CD 1 ATOM 65 O OE1 . GLU A 1 8 ? 11.484 3.066 9.520 1.00 16.03 ? 8 GLU A OE1 1 ATOM 66 O OE2 . GLU A 1 8 ? 12.286 5.102 9.692 1.00 19.91 ? 8 GLU A OE2 1 ATOM 67 N N . THR A 1 9 ? 16.671 4.586 6.960 1.00 3.35 ? 9 THR A N 1 ATOM 68 C CA . THR A 1 9 ? 17.907 4.015 7.504 1.00 2.16 ? 9 THR A CA 1 ATOM 69 C C . THR A 1 9 ? 18.298 4.871 8.683 1.00 1.01 ? 9 THR A C 1 ATOM 70 O O . THR A 1 9 ? 18.340 6.086 8.620 1.00 4.34 ? 9 THR A O 1 ATOM 71 C CB . THR A 1 9 ? 18.977 3.959 6.398 1.00 4.67 ? 9 THR A CB 1 ATOM 72 O OG1 . THR A 1 9 ? 20.194 3.305 6.865 1.00 8.16 ? 9 THR A OG1 1 ATOM 73 C CG2 . THR A 1 9 ? 19.314 5.353 5.870 1.00 5.55 ? 9 THR A CG2 1 ATOM 74 N N . GLN A 1 10 ? 18.656 4.210 9.908 1.00 4.34 ? 10 GLN A N 1 ATOM 75 C CA . GLN A 1 10 ? 19.252 4.836 10.824 1.00 7.46 ? 10 GLN A CA 1 ATOM 76 C C . GLN A 1 10 ? 20.696 5.179 10.828 1.00 6.75 ? 10 GLN A C 1 ATOM 77 O O . GLN A 1 10 ? 21.148 4.337 10.913 1.00 20.67 ? 10 GLN A O 1 ATOM 78 C CB . GLN A 1 10 ? 18.922 4.160 12.513 1.00 7.87 ? 10 GLN A CB 1 ATOM 79 C CG . GLN A 1 10 ? 17.517 3.874 12.572 1.00 7.33 ? 10 GLN A CG 1 ATOM 80 C CD . GLN A 1 10 ? 16.690 5.190 12.626 1.00 10.38 ? 10 GLN A CD 1 ATOM 81 O OE1 . GLN A 1 10 ? 17.026 6.224 13.343 1.00 10.09 ? 10 GLN A OE1 1 ATOM 82 N NE2 . GLN A 1 10 ? 15.504 5.081 11.962 1.00 7.79 ? 10 GLN A NE2 1 ATOM 83 O OXT . GLN A 1 10 ? 21.258 6.414 11.146 1.00 19.19 ? 10 GLN A OXT 1 HETATM 84 O O . HOH B 2 . ? 21.342 1.812 10.727 1.00 9.95 ? 101 HOH A O 1 HETATM 85 O O . HOH B 2 . ? 6.142 0.703 -11.050 0.50 4.14 ? 102 HOH A O 1 HETATM 86 O O A HOH B 2 . ? 6.754 7.135 -5.875 0.50 9.55 ? 103 HOH A O 1 HETATM 87 O O B HOH B 2 . ? 5.289 6.256 -5.714 0.50 7.83 ? 103 HOH A O 1 # 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 GLY 1 1 1 GLY GLY A . n A 1 2 TYR 2 2 2 TYR TYR A . n A 1 3 ARG 3 3 3 ARG ARG A . n A 1 4 VAL 4 4 4 VAL VAL A . n A 1 5 THR 5 5 5 THR THR A . n A 1 6 GLY 6 6 6 GLY GLY A . n A 1 7 TYR 7 7 7 TYR TYR A . n A 1 8 GLU 8 8 8 GLU GLU A . n A 1 9 THR 9 9 9 THR THR A . n A 1 10 GLN 10 10 10 GLN GLN A . n # _pdbx_contact_author.id 3 _pdbx_contact_author.email yone@spring8.or.jp _pdbx_contact_author.name_first Koji _pdbx_contact_author.name_last Yonekura _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-5520-4391 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 101 102 HOH HOH A . B 2 HOH 2 102 101 HOH HOH A . B 2 HOH 3 103 103 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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 x,y,z _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 2022-09-28 # _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 ? # 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 ? ? 'Paul D. Adams' PDAdams@lbl.gov ? ? ? ? C++ http://www.phenix-online.org/ ? PHENIX ? ? package 1.12_2829 1 ? 'data extraction' ? ? PDB deposit@deposit.rcsb.org 'Oct. 31, 2020' ? ? ? C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ? PDB_EXTRACT ? ? package 3.27 2 # _em_3d_fitting.entry_id 7VI4 _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol ? _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7VI4 _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles ? _em_3d_reconstruction.resolution ? _em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES' _em_3d_reconstruction.symmetry_type '3D CRYSTAL' _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 7.5 _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 'Region 2 peptides (G377-A386) of TIA-1 prion-like domain, A381T' _em_entity_assembly.source NATURAL _em_entity_assembly.type CELL _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 7VI4 _em_image_scans.id 1 _em_image_scans.dimension_height 4096 _em_image_scans.dimension_width 4096 _em_image_scans.frames_per_image 20 _em_image_scans.image_recording_id 1 _em_image_scans.sampling_size 6.5 _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 7VI4 _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'JEOL CRYO ARM 300' _em_imaging.mode DIFFRACTION _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model ? _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 200 _em_sample_support.grid_type 'Quantifoil R1.2/1.3' _em_sample_support.method ? _em_sample_support.film_material ? # _em_experiment.entry_id 7VI4 _em_experiment.id 1 _em_experiment.aggregation_state FILAMENT _em_experiment.reconstruction_method CRYSTALLOGRAPHY _em_experiment.entity_assembly_id 1 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N A GLN 10 ? ? CA A GLN 10 ? ? 1.259 1.459 -0.200 0.020 N 2 1 CA A GLN 10 ? ? CB A GLN 10 ? ? 1.849 1.535 0.314 0.022 N 3 1 C A GLN 10 ? ? O A GLN 10 ? ? 0.959 1.229 -0.270 0.019 N 4 1 C A GLN 10 ? ? OXT A GLN 10 ? ? 1.394 1.229 0.165 0.019 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_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 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CD A ARG 3 ? ? NE A ARG 3 ? ? CZ A ARG 3 ? ? 134.75 123.60 11.15 1.40 N 2 1 NE A ARG 3 ? ? CZ A ARG 3 ? ? NH1 A ARG 3 ? ? 125.93 120.30 5.63 0.50 N 3 1 NE A ARG 3 ? ? CZ A ARG 3 ? ? NH2 A ARG 3 ? ? 116.07 120.30 -4.23 0.50 N 4 1 CA A GLN 10 ? ? C A GLN 10 ? ? O A GLN 10 ? ? 104.82 120.10 -15.28 2.10 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id ARG _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 3 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.191 _pdbx_validate_planes.type 'SIDE CHAIN' # _em_3d_crystal_entity.id 1 _em_3d_crystal_entity.image_processing_id 1 _em_3d_crystal_entity.angle_alpha 90 _em_3d_crystal_entity.angle_beta 116.15 _em_3d_crystal_entity.angle_gamma 90 _em_3d_crystal_entity.length_a 30.68 _em_3d_crystal_entity.length_b 9.63 _em_3d_crystal_entity.length_c 26.25 _em_3d_crystal_entity.space_group_name C2 _em_3d_crystal_entity.space_group_num 5 # loop_ _em_buffer_component.buffer_id _em_buffer_component.id _em_buffer_component.concentration _em_buffer_component.concentration_units _em_buffer_component.formula _em_buffer_component.name 1 1 0.2 M '(NH4)2HPO4' 'ammonium phosphate' 1 2 40 % C6H14O2 MPD 1 3 0.1 M C8H18N2O4S HEPES # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type NONE _em_ctf_correction.details ? # _em_diffraction.id 1 _em_diffraction.camera_length 1060 _em_diffraction.imaging_id 1 _em_diffraction.tilt_angle_list ? # _em_diffraction_shell.id 1 _em_diffraction_shell.em_diffraction_stats_id 1 _em_diffraction_shell.fourier_space_coverage 77.7 _em_diffraction_shell.high_resolution 0.95 _em_diffraction_shell.low_resolution 15.1 _em_diffraction_shell.multiplicity 27.0 _em_diffraction_shell.num_structure_factors 3555 _em_diffraction_shell.phase_residual 34.66 # _em_diffraction_stats.id 1 _em_diffraction_stats.details ? _em_diffraction_stats.image_processing_id 1 _em_diffraction_stats.fourier_space_coverage 77.7 _em_diffraction_stats.high_resolution 0.95 _em_diffraction_stats.num_intensities_measured 95985 _em_diffraction_stats.num_structure_factors 3555 _em_diffraction_stats.overall_phase_error ? _em_diffraction_stats.overall_phase_residual ? _em_diffraction_stats.phase_error_rejection_criteria None _em_diffraction_stats.r_merge 37.3 _em_diffraction_stats.r_sym ? # _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 32630 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'synthetic construct' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _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 0.02 _em_image_recording.average_exposure_time 1.0 _em_image_recording.details ? _em_image_recording.detector_mode INTEGRATING _em_image_recording.film_or_detector_model 'DIRECT ELECTRON DE-64 (8k x 8k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _em_image_recording.avg_electron_dose_per_subtomogram ? # 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 'IMAGE ACQUISITION' ? ? ? ? ? ? 2 MASKING ? ? ? ? ? ? 3 'CTF CORRECTION' ? ? ? ? ? ? 4 'LAYERLINE INDEXING' ? ? ? ? ? ? 5 'DIFFRACTION INDEXING' ? ? ? ? ? ? 6 'MODEL FITTING' ? ? ? ? 1 ? 7 OTHER ? ? ? ? ? ? 8 'MOLECULAR REPLACEMENT' ? ? ? ? ? ? 9 'LATTICE DISTORTION CORRECTION' ? ? ? ? ? ? 10 'SYMMETRY DETERMINATION' ? ? ? ? ? ? 11 'CRYSTALLOGRAPHY MERGING' ? ? ? ? ? ? 12 RECONSTRUCTION ? ? ? ? ? ? 13 'MODEL REFINEMENT' ? ? ? ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 10 _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied NO # 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 JP19K06584 1 'Japan Science and Technology' Japan JPMJCR1762 2 'Japan Science and Technology' Japan JPMJMI20G5 3 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' Japan JPMXS0421700121 4 'Japan Agency for Medical Research and Development (AMED)' Japan ? 5 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_related_exp_data_set.data_reference 10.5281/zenodo.6921032 _pdbx_related_exp_data_set.data_set_type 'diffraction image data' _pdbx_related_exp_data_set.details ? _pdbx_related_exp_data_set.metadata_reference ? _pdbx_related_exp_data_set.ordinal 1 # _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 ? #