data_7VI5
#
_entry.id 7VI5
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.380
_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 7VI5 pdb_00007vi5 10.2210/pdb7vi5/pdb
WWPDB D_1300024728 ? ?
#
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.entry_id 7VI5
_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 90.000
_cell.angle_beta_esd ?
_cell.angle_gamma 120.000
_cell.angle_gamma_esd ?
_cell.entry_id 7VI5
_cell.details ?
_cell.formula_units_Z ?
_cell.length_a 43.570
_cell.length_a_esd ?
_cell.length_b 43.570
_cell.length_b_esd ?
_cell.length_c 9.630
_cell.length_c_esd ?
_cell.volume ?
_cell.volume_esd ?
_cell.Z_PDB 6
_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 7VI5
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 170
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 65'
_symmetry.pdbx_full_space_group_name_H-M ?
#
_entity.id 1
_entity.type polymer
_entity.src_method syn
_entity.pdbx_description 'TIA-1 prion-like domain'
_entity.formula_weight 1144.215
_entity.pdbx_number_of_molecules 1
_entity.pdbx_ec ?
_entity.pdbx_mutation ?
_entity.pdbx_fragment ?
_entity.details ?
#
_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 GYRVAGYETQ
_entity_poly.pdbx_seq_one_letter_code_can GYRVAGYETQ
_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 ALA 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 7VI5
_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
#
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
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 7VI5
_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 33.340
_refine.B_iso_mean 12.1368
_refine.B_iso_min 0.000
_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 7VI5
_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 1.7610
_refine.ls_d_res_low 18.8660
_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 1149
_refine.ls_number_reflns_R_free 114
_refine.ls_number_reflns_R_work 1035
_refine.ls_number_restraints ?
_refine.ls_percent_reflns_obs 99.9100
_refine.ls_percent_reflns_R_free 9.9200
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs 0.2839
_refine.ls_R_factor_R_free 0.3473
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_R_factor_R_work 0.2772
_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 1.420
_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 'MOLECULAR REPLACEMENT'
_refine.pdbx_starting_model 7VI4
_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 19.2200
_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 0.2900
_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 1.76
_refine_hist.d_res_low 18.87
_refine_hist.number_atoms_solvent 0
_refine_hist.number_atoms_total 76
_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 ?
_refine_hist.pdbx_number_atoms_protein ?
_refine_hist.pdbx_number_atoms_nucleic_acid ?
_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' ? 0.009 ? 77 ? f_bond_d ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 1.072 ? 103 ? f_angle_d ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.080 ? 10 ? f_chiral_restr ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.005 ? 13 ? f_plane_restr ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 9.935 ? 25 ? 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' 1.761 1.8234 . . 12 97 100.0000 . . . 0.2729 0.0000 0.2168 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 1.8234 1.8964 . . 11 111 100.0000 . . . 0.5376 0.0000 0.2337 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 1.8964 1.9826 . . 11 98 100.0000 . . . 0.3799 0.0000 0.2855 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 1.9826 2.0870 . . 12 94 100.0000 . . . 0.2723 0.0000 0.2727 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 2.0870 2.2175 . . 9 97 100.0000 . . . 0.3692 0.0000 0.3267 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 2.2175 2.3884 . . 14 111 100.0000 . . . 0.3265 0.0000 0.2875 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 2.3884 2.6282 . . 9 100 100.0000 . . . 0.4613 0.0000 0.2879 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 2.6282 3.0072 . . 10 104 100.0000 . . . 0.3853 0.0000 0.2997 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 3.0072 3.7838 . . 11 106 100.0000 . . . 0.3303 0.0000 0.2888 . . . . . . . . . . .
'ELECTRON CRYSTALLOGRAPHY' 3.7838 18.866 . . 15 117 99.0000 . . . 0.2532 0.0000 0.2845 . . . . . . . . . . .
#
_struct.entry_id 7VI5
_struct.title 'Electron crystallographic structure of TIA-1 prion-like domain, wild type sequence'
_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 7VI5
_struct_keywords.text 'ALS, prion, fibril, PROTEIN FIBRIL'
_struct_keywords.pdbx_keywords 'PROTEIN FIBRIL'
#
_struct_asym.id A
_struct_asym.pdbx_blank_PDB_chainid_flag N
_struct_asym.pdbx_modified N
_struct_asym.entity_id 1
_struct_asym.details ?
#
_atom_sites.entry_id 7VI5
_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] 0.022952
_atom_sites.fract_transf_matrix[1][2] 0.013251
_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] 0.026502
_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] 0.103842
_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 ? 19.379 33.391 -0.960 1.00 3.57 ? 1 GLY A N 1
ATOM 2 C CA . GLY A 1 1 ? 18.513 32.353 -1.511 1.00 16.06 ? 1 GLY A CA 1
ATOM 3 C C . GLY A 1 1 ? 18.103 31.280 -0.517 1.00 6.28 ? 1 GLY A C 1
ATOM 4 O O . GLY A 1 1 ? 18.375 31.379 0.688 1.00 5.94 ? 1 GLY A O 1
ATOM 5 N N . TYR A 1 2 ? 17.448 30.226 -1.008 1.00 3.68 ? 2 TYR A N 1
ATOM 6 C CA . TYR A 1 2 ? 16.939 29.164 -0.140 1.00 15.22 ? 2 TYR A CA 1
ATOM 7 C C . TYR A 1 2 ? 16.703 27.923 -0.983 1.00 5.61 ? 2 TYR A C 1
ATOM 8 O O . TYR A 1 2 ? 16.715 27.971 -2.214 1.00 11.76 ? 2 TYR A O 1
ATOM 9 C CB . TYR A 1 2 ? 15.628 29.560 0.554 1.00 6.40 ? 2 TYR A CB 1
ATOM 10 C CG . TYR A 1 2 ? 14.498 29.660 -0.442 1.00 9.68 ? 2 TYR A CG 1
ATOM 11 C CD1 . TYR A 1 2 ? 13.651 28.587 -0.662 1.00 12.41 ? 2 TYR A CD1 1
ATOM 12 C CD2 . TYR A 1 2 ? 14.292 30.816 -1.183 1.00 13.24 ? 2 TYR A CD2 1
ATOM 13 C CE1 . TYR A 1 2 ? 12.630 28.652 -1.573 1.00 15.05 ? 2 TYR A CE1 1
ATOM 14 C CE2 . TYR A 1 2 ? 13.264 30.895 -2.116 1.00 18.51 ? 2 TYR A CE2 1
ATOM 15 C CZ . TYR A 1 2 ? 12.431 29.806 -2.302 1.00 13.94 ? 2 TYR A CZ 1
ATOM 16 O OH . TYR A 1 2 ? 11.401 29.855 -3.204 1.00 21.28 ? 2 TYR A OH 1
ATOM 17 N N . ARG A 1 3 ? 16.484 26.808 -0.296 1.00 2.49 ? 3 ARG A N 1
ATOM 18 C CA . ARG A 1 3 ? 16.184 25.536 -0.930 1.00 7.30 ? 3 ARG A CA 1
ATOM 19 C C . ARG A 1 3 ? 15.086 24.843 -0.142 1.00 10.10 ? 3 ARG A C 1
ATOM 20 O O . ARG A 1 3 ? 14.959 25.067 1.067 1.00 0.01 ? 3 ARG A O 1
ATOM 21 C CB . ARG A 1 3 ? 17.439 24.649 -1.008 1.00 27.37 ? 3 ARG A CB 1
ATOM 22 C CG . ARG A 1 3 ? 18.090 24.348 0.341 1.00 9.88 ? 3 ARG A CG 1
ATOM 23 C CD . ARG A 1 3 ? 19.485 23.776 0.078 1.00 18.49 ? 3 ARG A CD 1
ATOM 24 N NE . ARG A 1 3 ? 20.184 23.227 1.233 1.00 24.97 ? 3 ARG A NE 1
ATOM 25 C CZ . ARG A 1 3 ? 20.872 23.939 2.121 1.00 33.34 ? 3 ARG A CZ 1
ATOM 26 N NH1 . ARG A 1 3 ? 20.959 25.252 2.009 1.00 18.30 ? 3 ARG A NH1 1
ATOM 27 N NH2 . ARG A 1 3 ? 21.480 23.326 3.129 1.00 27.58 ? 3 ARG A NH2 1
ATOM 28 N N . VAL A 1 4 ? 14.337 23.969 -0.827 1.00 8.53 ? 4 VAL A N 1
ATOM 29 C CA . VAL A 1 4 ? 13.126 23.345 -0.288 1.00 5.22 ? 4 VAL A CA 1
ATOM 30 C C . VAL A 1 4 ? 12.799 22.100 -1.114 1.00 6.70 ? 4 VAL A C 1
ATOM 31 O O . VAL A 1 4 ? 13.076 22.041 -2.318 1.00 7.66 ? 4 VAL A O 1
ATOM 32 C CB . VAL A 1 4 ? 11.942 24.360 -0.245 1.00 0.45 ? 4 VAL A CB 1
ATOM 33 C CG1 . VAL A 1 4 ? 11.577 24.901 -1.601 1.00 4.90 ? 4 VAL A CG1 1
ATOM 34 C CG2 . VAL A 1 4 ? 10.738 23.774 0.538 1.00 9.39 ? 4 VAL A CG2 1
ATOM 35 N N . ALA A 1 5 ? 12.187 21.108 -0.466 1.00 8.94 ? 5 ALA A N 1
ATOM 36 C CA . ALA A 1 5 ? 11.919 19.824 -1.116 1.00 3.32 ? 5 ALA A CA 1
ATOM 37 C C . ALA A 1 5 ? 10.873 19.076 -0.296 1.00 5.49 ? 5 ALA A C 1
ATOM 38 O O . ALA A 1 5 ? 10.671 19.351 0.896 1.00 3.57 ? 5 ALA A O 1
ATOM 39 C CB . ALA A 1 5 ? 13.212 19.018 -1.286 1.00 3.32 ? 5 ALA A CB 1
ATOM 40 N N . GLY A 1 6 ? 10.187 18.157 -0.959 1.00 3.42 ? 6 GLY A N 1
ATOM 41 C CA . GLY A 1 6 ? 9.097 17.411 -0.343 1.00 9.04 ? 6 GLY A CA 1
ATOM 42 C C . GLY A 1 6 ? 8.944 16.056 -0.996 1.00 11.52 ? 6 GLY A C 1
ATOM 43 O O . GLY A 1 6 ? 9.286 15.871 -2.168 1.00 12.84 ? 6 GLY A O 1
ATOM 44 N N . TYR A 1 7 ? 8.403 15.103 -0.239 1.00 6.08 ? 7 TYR A N 1
ATOM 45 C CA . TYR A 1 7 ? 8.168 13.752 -0.752 1.00 5.60 ? 7 TYR A CA 1
ATOM 46 C C . TYR A 1 7 ? 7.021 13.139 0.032 1.00 12.40 ? 7 TYR A C 1
ATOM 47 O O . TYR A 1 7 ? 6.880 13.355 1.246 1.00 3.09 ? 7 TYR A O 1
ATOM 48 C CB . TYR A 1 7 ? 9.431 12.854 -0.663 1.00 6.92 ? 7 TYR A CB 1
ATOM 49 C CG . TYR A 1 7 ? 9.253 11.389 -1.057 1.00 9.18 ? 7 TYR A CG 1
ATOM 50 C CD1 . TYR A 1 7 ? 9.775 10.884 -2.250 1.00 7.61 ? 7 TYR A CD1 1
ATOM 51 C CD2 . TYR A 1 7 ? 8.569 10.502 -0.224 1.00 19.78 ? 7 TYR A CD2 1
ATOM 52 C CE1 . TYR A 1 7 ? 9.591 9.545 -2.595 1.00 9.76 ? 7 TYR A CE1 1
ATOM 53 C CE2 . TYR A 1 7 ? 8.387 9.184 -0.554 1.00 15.17 ? 7 TYR A CE2 1
ATOM 54 C CZ . TYR A 1 7 ? 8.888 8.695 -1.723 1.00 3.39 ? 7 TYR A CZ 1
ATOM 55 O OH . TYR A 1 7 ? 8.679 7.363 -2.015 1.00 8.22 ? 7 TYR A OH 1
ATOM 56 N N . GLU A 1 8 ? 6.224 12.342 -0.676 1.00 5.25 ? 8 GLU A N 1
ATOM 57 C CA . GLU A 1 8 ? 5.042 11.717 -0.111 1.00 10.43 ? 8 GLU A CA 1
ATOM 58 C C . GLU A 1 8 ? 4.698 10.489 -0.935 1.00 17.41 ? 8 GLU A C 1
ATOM 59 O O . GLU A 1 8 ? 4.747 10.529 -2.171 1.00 6.33 ? 8 GLU A O 1
ATOM 60 C CB . GLU A 1 8 ? 3.867 12.697 -0.104 1.00 11.03 ? 8 GLU A CB 1
ATOM 61 C CG . GLU A 1 8 ? 2.678 12.291 0.712 1.00 24.83 ? 8 GLU A CG 1
ATOM 62 C CD . GLU A 1 8 ? 1.659 13.406 0.774 1.00 25.57 ? 8 GLU A CD 1
ATOM 63 O OE1 . GLU A 1 8 ? 2.071 14.579 0.793 1.00 25.01 ? 8 GLU A OE1 1
ATOM 64 O OE2 . GLU A 1 8 ? 0.451 13.118 0.742 1.00 17.96 ? 8 GLU A OE2 1
ATOM 65 N N . THR A 1 9 ? 4.343 9.405 -0.242 1.00 13.21 ? 9 THR A N 1
ATOM 66 C CA . THR A 1 9 ? 3.770 8.245 -0.912 1.00 23.57 ? 9 THR A CA 1
ATOM 67 C C . THR A 1 9 ? 2.436 8.624 -1.553 1.00 15.62 ? 9 THR A C 1
ATOM 68 O O . THR A 1 9 ? 1.697 9.459 -1.033 1.00 15.23 ? 9 THR A O 1
ATOM 69 C CB . THR A 1 9 ? 3.605 7.093 0.089 1.00 18.24 ? 9 THR A CB 1
ATOM 70 O OG1 . THR A 1 9 ? 4.899 6.659 0.522 1.00 10.95 ? 9 THR A OG1 1
ATOM 71 C CG2 . THR A 1 9 ? 2.871 5.889 -0.534 1.00 19.54 ? 9 THR A CG2 1
ATOM 72 N N . GLN A 1 10 ? 2.161 8.044 -2.721 1.00 19.48 ? 10 GLN A N 1
ATOM 73 C CA . GLN A 1 10 ? 0.915 8.264 -3.471 1.00 12.49 ? 10 GLN A CA 1
ATOM 74 C C . GLN A 1 10 ? 0.801 9.705 -3.923 1.00 21.03 ? 10 GLN A C 1
ATOM 75 O O . GLN A 1 10 ? 1.432 10.106 -4.906 1.00 24.92 ? 10 GLN A O 1
ATOM 76 C CB . GLN A 1 10 ? -0.310 7.864 -2.642 1.00 14.34 ? 10 GLN A CB 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 ALA 5 5 5 ALA ALA 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
#
_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
#
_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
#
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
1 'Structure model' 1 0 2022-09-28
2 'Structure model' 1 1 2023-11-29
#
_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_
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
_pdbx_audit_revision_group.group
1 2 'Structure model' 'Data collection'
2 2 'Structure model' 'Refinement description'
#
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 2 'Structure model' chem_comp_atom
2 2 'Structure model' chem_comp_bond
3 2 'Structure model' pdbx_initial_refinement_model
#
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 ? ? ? 1.12_2829
1
? 'data scaling' ? ? 'Wolfgang Kabsch' ? ? ? ? ? ?
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? XSCALE ? ? package . 2
? 'data extraction' ? ? PDB deposit@deposit.rcsb.org 'Oct. 31, 2020' ? ? ? C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ? PDB_EXTRACT ? ? package 3.27 3
#
_em_3d_fitting.entry_id 7VI5
_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 7VI5
_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-Q386) of TIA-1 prion-like domain, wild-type'
_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 7VI5
_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 ?
_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 7VI5
_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 7VI5
_em_experiment.id 1
_em_experiment.aggregation_state FILAMENT
_em_experiment.reconstruction_method CRYSTALLOGRAPHY
_em_experiment.entity_assembly_id 1
#
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 GLN 10 ? CG ? A GLN 10 CG
2 1 Y 1 A GLN 10 ? CD ? A GLN 10 CD
3 1 Y 1 A GLN 10 ? OE1 ? A GLN 10 OE1
4 1 Y 1 A GLN 10 ? NE2 ? A GLN 10 NE2
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
ALA N N N N 1
ALA CA C N S 2
ALA C C N N 3
ALA O O N N 4
ALA CB C N N 5
ALA OXT O N N 6
ALA H H N N 7
ALA H2 H N N 8
ALA HA H N N 9
ALA HB1 H N N 10
ALA HB2 H N N 11
ALA HB3 H N N 12
ALA HXT H N N 13
ARG N N N N 14
ARG CA C N S 15
ARG C C N N 16
ARG O O N N 17
ARG CB C N N 18
ARG CG C N N 19
ARG CD C N N 20
ARG NE N N N 21
ARG CZ C N N 22
ARG NH1 N N N 23
ARG NH2 N N N 24
ARG OXT O N N 25
ARG H H N N 26
ARG H2 H N N 27
ARG HA H N N 28
ARG HB2 H N N 29
ARG HB3 H N N 30
ARG HG2 H N N 31
ARG HG3 H N N 32
ARG HD2 H N N 33
ARG HD3 H N N 34
ARG HE H N N 35
ARG HH11 H N N 36
ARG HH12 H N N 37
ARG HH21 H N N 38
ARG HH22 H N N 39
ARG HXT H N N 40
GLN N N N N 41
GLN CA C N S 42
GLN C C N N 43
GLN O O N N 44
GLN CB C N N 45
GLN CG C N N 46
GLN CD C N N 47
GLN OE1 O N N 48
GLN NE2 N N N 49
GLN OXT O N N 50
GLN H H N N 51
GLN H2 H N N 52
GLN HA H N N 53
GLN HB2 H N N 54
GLN HB3 H N N 55
GLN HG2 H N N 56
GLN HG3 H N N 57
GLN HE21 H N N 58
GLN HE22 H N N 59
GLN HXT H N N 60
GLU N N N N 61
GLU CA C N S 62
GLU C C N N 63
GLU O O N N 64
GLU CB C N N 65
GLU CG C N N 66
GLU CD C N N 67
GLU OE1 O N N 68
GLU OE2 O N N 69
GLU OXT O N N 70
GLU H H N N 71
GLU H2 H N N 72
GLU HA H N N 73
GLU HB2 H N N 74
GLU HB3 H N N 75
GLU HG2 H N N 76
GLU HG3 H N N 77
GLU HE2 H N N 78
GLU HXT H N N 79
GLY N N N N 80
GLY CA C N N 81
GLY C C N N 82
GLY O O N N 83
GLY OXT O N N 84
GLY H H N N 85
GLY H2 H N N 86
GLY HA2 H N N 87
GLY HA3 H N N 88
GLY HXT H N N 89
THR N N N N 90
THR CA C N S 91
THR C C N N 92
THR O O N N 93
THR CB C N R 94
THR OG1 O N N 95
THR CG2 C N N 96
THR OXT O N N 97
THR H H N N 98
THR H2 H N N 99
THR HA H N N 100
THR HB H N N 101
THR HG1 H N N 102
THR HG21 H N N 103
THR HG22 H N N 104
THR HG23 H N N 105
THR HXT H N N 106
TYR N N N N 107
TYR CA C N S 108
TYR C C N N 109
TYR O O N N 110
TYR CB C N N 111
TYR CG C Y N 112
TYR CD1 C Y N 113
TYR CD2 C Y N 114
TYR CE1 C Y N 115
TYR CE2 C Y N 116
TYR CZ C Y N 117
TYR OH O N N 118
TYR OXT O N N 119
TYR H H N N 120
TYR H2 H N N 121
TYR HA H N N 122
TYR HB2 H N N 123
TYR HB3 H N N 124
TYR HD1 H N N 125
TYR HD2 H N N 126
TYR HE1 H N N 127
TYR HE2 H N N 128
TYR HH H N N 129
TYR HXT H N N 130
VAL N N N N 131
VAL CA C N S 132
VAL C C N N 133
VAL O O N N 134
VAL CB C N N 135
VAL CG1 C N N 136
VAL CG2 C N N 137
VAL OXT O N N 138
VAL H H N N 139
VAL H2 H N N 140
VAL HA H N N 141
VAL HB H N N 142
VAL HG11 H N N 143
VAL HG12 H N N 144
VAL HG13 H N N 145
VAL HG21 H N N 146
VAL HG22 H N N 147
VAL HG23 H N N 148
VAL HXT H N N 149
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
ALA N CA sing N N 1
ALA N H sing N N 2
ALA N H2 sing N N 3
ALA CA C sing N N 4
ALA CA CB sing N N 5
ALA CA HA sing N N 6
ALA C O doub N N 7
ALA C OXT sing N N 8
ALA CB HB1 sing N N 9
ALA CB HB2 sing N N 10
ALA CB HB3 sing N N 11
ALA OXT HXT sing N N 12
ARG N CA sing N N 13
ARG N H sing N N 14
ARG N H2 sing N N 15
ARG CA C sing N N 16
ARG CA CB sing N N 17
ARG CA HA sing N N 18
ARG C O doub N N 19
ARG C OXT sing N N 20
ARG CB CG sing N N 21
ARG CB HB2 sing N N 22
ARG CB HB3 sing N N 23
ARG CG CD sing N N 24
ARG CG HG2 sing N N 25
ARG CG HG3 sing N N 26
ARG CD NE sing N N 27
ARG CD HD2 sing N N 28
ARG CD HD3 sing N N 29
ARG NE CZ sing N N 30
ARG NE HE sing N N 31
ARG CZ NH1 sing N N 32
ARG CZ NH2 doub N N 33
ARG NH1 HH11 sing N N 34
ARG NH1 HH12 sing N N 35
ARG NH2 HH21 sing N N 36
ARG NH2 HH22 sing N N 37
ARG OXT HXT sing N N 38
GLN N CA sing N N 39
GLN N H sing N N 40
GLN N H2 sing N N 41
GLN CA C sing N N 42
GLN CA CB sing N N 43
GLN CA HA sing N N 44
GLN C O doub N N 45
GLN C OXT sing N N 46
GLN CB CG sing N N 47
GLN CB HB2 sing N N 48
GLN CB HB3 sing N N 49
GLN CG CD sing N N 50
GLN CG HG2 sing N N 51
GLN CG HG3 sing N N 52
GLN CD OE1 doub N N 53
GLN CD NE2 sing N N 54
GLN NE2 HE21 sing N N 55
GLN NE2 HE22 sing N N 56
GLN OXT HXT sing N N 57
GLU N CA sing N N 58
GLU N H sing N N 59
GLU N H2 sing N N 60
GLU CA C sing N N 61
GLU CA CB sing N N 62
GLU CA HA sing N N 63
GLU C O doub N N 64
GLU C OXT sing N N 65
GLU CB CG sing N N 66
GLU CB HB2 sing N N 67
GLU CB HB3 sing N N 68
GLU CG CD sing N N 69
GLU CG HG2 sing N N 70
GLU CG HG3 sing N N 71
GLU CD OE1 doub N N 72
GLU CD OE2 sing N N 73
GLU OE2 HE2 sing N N 74
GLU OXT HXT sing N N 75
GLY N CA sing N N 76
GLY N H sing N N 77
GLY N H2 sing N N 78
GLY CA C sing N N 79
GLY CA HA2 sing N N 80
GLY CA HA3 sing N N 81
GLY C O doub N N 82
GLY C OXT sing N N 83
GLY OXT HXT sing N N 84
THR N CA sing N N 85
THR N H sing N N 86
THR N H2 sing N N 87
THR CA C sing N N 88
THR CA CB sing N N 89
THR CA HA sing N N 90
THR C O doub N N 91
THR C OXT sing N N 92
THR CB OG1 sing N N 93
THR CB CG2 sing N N 94
THR CB HB sing N N 95
THR OG1 HG1 sing N N 96
THR CG2 HG21 sing N N 97
THR CG2 HG22 sing N N 98
THR CG2 HG23 sing N N 99
THR OXT HXT sing N N 100
TYR N CA sing N N 101
TYR N H sing N N 102
TYR N H2 sing N N 103
TYR CA C sing N N 104
TYR CA CB sing N N 105
TYR CA HA sing N N 106
TYR C O doub N N 107
TYR C OXT sing N N 108
TYR CB CG sing N N 109
TYR CB HB2 sing N N 110
TYR CB HB3 sing N N 111
TYR CG CD1 doub Y N 112
TYR CG CD2 sing Y N 113
TYR CD1 CE1 sing Y N 114
TYR CD1 HD1 sing N N 115
TYR CD2 CE2 doub Y N 116
TYR CD2 HD2 sing N N 117
TYR CE1 CZ doub Y N 118
TYR CE1 HE1 sing N N 119
TYR CE2 CZ sing Y N 120
TYR CE2 HE2 sing N N 121
TYR CZ OH sing N N 122
TYR OH HH sing N N 123
TYR OXT HXT sing N N 124
VAL N CA sing N N 125
VAL N H sing N N 126
VAL N H2 sing N N 127
VAL CA C sing N N 128
VAL CA CB sing N N 129
VAL CA HA sing N N 130
VAL C O doub N N 131
VAL C OXT sing N N 132
VAL CB CG1 sing N N 133
VAL CB CG2 sing N N 134
VAL CB HB sing N N 135
VAL CG1 HG11 sing N N 136
VAL CG1 HG12 sing N N 137
VAL CG1 HG13 sing N N 138
VAL CG2 HG21 sing N N 139
VAL CG2 HG22 sing N N 140
VAL CG2 HG23 sing N N 141
VAL OXT HXT sing N N 142
#
_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 90
_em_3d_crystal_entity.angle_gamma 120
_em_3d_crystal_entity.length_a 43.57
_em_3d_crystal_entity.length_b 43.57
_em_3d_crystal_entity.length_c 9.63
_em_3d_crystal_entity.space_group_name 'P 65'
_em_3d_crystal_entity.space_group_num 170
#
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 45 % 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 1058
_em_diffraction.imaging_id 1
_em_diffraction.tilt_angle_list '-68 to +68, 1 deg./frame'
#
_em_diffraction_shell.id 1
_em_diffraction_shell.em_diffraction_stats_id 1
_em_diffraction_shell.fourier_space_coverage 99.7
_em_diffraction_shell.high_resolution 1.76
_em_diffraction_shell.low_resolution 18.9
_em_diffraction_shell.multiplicity 22.4
_em_diffraction_shell.num_structure_factors 1149
_em_diffraction_shell.phase_residual 33.9
#
_em_diffraction_stats.id 1
_em_diffraction_stats.details ?
_em_diffraction_stats.image_processing_id 1
_em_diffraction_stats.fourier_space_coverage 99.7
_em_diffraction_stats.high_resolution 1.76
_em_diffraction_stats.num_intensities_measured 25738
_em_diffraction_stats.num_structure_factors 1149
_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 34.5
_em_diffraction_stats.r_sym ?
#
_em_entity_assembly_naturalsource.id 1
_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 'SERIES ALIGNMENT' ? ? ? 1 1 1
2 MASKING ? ? ? ? ? ?
3 'CTF CORRECTION' ? ? ? 1 ? ?
4 'LAYERLINE INDEXING' ? ? ? ? ? ?
5 'DIFFRACTION INDEXING' ? ? ? ? ? ?
6 'MODEL FITTING' ? ? ? ? 1 ?
7 OTHER ? ? ? ? ? ?
8 'MOLECULAR REPLACEMENT' ? ? ? 1 ? ?
9 'LATTICE DISTORTION CORRECTION' ? ? ? 1 ? ?
10 'SYMMETRY DETERMINATION' ? ? ? 1 ? ?
11 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 ? ?
12 RECONSTRUCTION ? ? ? 1 ? ?
13 'MODEL REFINEMENT' ? PHENIX ? ? 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
'Japan Agency for Medical Research and Development (AMED)' Japan JPMXS0421700121 4
'Japan Agency for Medical Research and Development (AMED)' Japan ? 5
#
_pdbx_initial_refinement_model.id 1
_pdbx_initial_refinement_model.entity_id_list ?
_pdbx_initial_refinement_model.type 'experimental model'
_pdbx_initial_refinement_model.source_name PDB
_pdbx_initial_refinement_model.accession_code 7VI4
_pdbx_initial_refinement_model.details ?
#
_pdbx_related_exp_data_set.data_reference 10.5281/zenodo.6923395
_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 ?
#