data_9NEQ # _entry.id 9NEQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.410 _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 9NEQ pdb_00009neq 10.2210/pdb9neq/pdb WWPDB D_1000293214 ? ? EMDB EMD-49330 ? ? # 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 2026-03-11 ? 2 'EM metadata' 1 0 2026-03-11 ? 3 'Half map' 1 0 2026-03-11 1 4 'Half map' 1 0 2026-03-11 2 5 Image 1 0 2026-03-11 ? 6 'Primary map' 1 0 2026-03-11 ? # 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 'Half map' repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 Image repository 'Initial release' ? ? 6 6 '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 9NEQ _pdbx_database_status.recvd_initial_deposition_date 2025-02-20 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM of NBD-L4pY nanofibers at 1.25mM concentration' _pdbx_database_related.db_id EMD-49330 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email fw2@uab.edu _pdbx_contact_author.name_first Fengbin _pdbx_contact_author.name_last Wang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-1008-663X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Zia, A.' 1 ? 'Guo, J.' 2 ? 'Xu, B.' 3 ? 'Wang, F.' 4 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Cryo-EM of NBD-L4pY nanofibers at 1.25mM concentration' _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 'Zia, A.' 1 ? primary 'Guo, J.' 2 ? primary 'Xu, B.' 3 ? primary 'Wang, F.' 4 ? # 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 '(UQ4)LLLL(PTR)' 947.968 3 ? ? ? ? 2 non-polymer syn 'N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-beta-alanine' 252.184 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(UQ4)LLLL(PTR)' _entity_poly.pdbx_seq_one_letter_code_can XLLLLY _entity_poly.pdbx_strand_id A,B,C _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-beta-alanine' _pdbx_entity_nonpoly.comp_id UQ4 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 UQ4 n 1 2 LEU n 1 3 LEU n 1 4 LEU n 1 5 LEU n 1 6 PTR 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 6 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.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 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 PTR 'L-peptide linking' n O-PHOSPHOTYROSINE PHOSPHONOTYROSINE 'C9 H12 N O6 P' 261.168 UQ4 non-polymer . 'N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-beta-alanine' ? 'C9 H8 N4 O5' 252.184 # 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 UQ4 1 1 1 UQ4 UQ4 A . n A 1 2 LEU 2 2 2 LEU LEU A . n A 1 3 LEU 3 3 3 LEU LEU A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 PTR 6 6 ? ? ? A . n B 1 1 UQ4 1 1 1 UQ4 UQ4 B . n B 1 2 LEU 2 2 2 LEU LEU B . n B 1 3 LEU 3 3 3 LEU LEU B . n B 1 4 LEU 4 4 4 LEU LEU B . n B 1 5 LEU 5 5 5 LEU LEU B . n B 1 6 PTR 6 6 ? ? ? B . n C 1 1 UQ4 1 1 1 UQ4 UQ4 C . n C 1 2 LEU 2 2 2 LEU LEU C . n C 1 3 LEU 3 3 3 LEU LEU C . n C 1 4 LEU 4 4 4 LEU LEU C . n C 1 5 LEU 5 5 5 LEU LEU C . n C 1 6 PTR 6 6 ? ? ? C . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id UQ4 _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id UQ4 _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_nonpoly_scheme.asym_id D _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id UQ4 _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 2 _pdbx_nonpoly_scheme.pdb_mon_id UQ4 _pdbx_nonpoly_scheme.auth_mon_id UQ4 _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag N _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id B _pdbx_unobs_or_zero_occ_atoms.auth_comp_id UQ4 _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 101 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id OXT _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id D _pdbx_unobs_or_zero_occ_atoms.label_comp_id UQ4 _pdbx_unobs_or_zero_occ_atoms.label_seq_id 1 _pdbx_unobs_or_zero_occ_atoms.label_atom_id OXT # _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 9NEQ _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 9NEQ _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 9NEQ _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 9NEQ _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 'REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.004 ? 13440 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 1.066 ? 18240 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 26.218 ? 1920 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.056 ? 1920 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.001 ? 1600 ? f_plane_restr ? ? # _struct.entry_id 9NEQ _struct.title 'Cryo-EM of NBD-L4pY nanofibers at 1.25mM concentration' _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 9NEQ _struct_keywords.text 'peptide fiber, helical polymer, 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 1 ? C N N 1 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9NEQ _struct_ref.pdbx_db_accession 9NEQ _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 9NEQ A 1 ? 6 ? 9NEQ 1 ? 6 ? 1 6 2 1 9NEQ B 1 ? 6 ? 9NEQ 1 ? 6 ? 1 6 3 1 9NEQ C 1 ? 6 ? 9NEQ 1 ? 6 ? 1 6 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'representative helical assembly' ? 24-meric 24 2 'helical asymmetric unit' ? trimeric 3 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-8)' A,B,C,D 2 1 A,B,C,D # _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' # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 2 'helical symmetry operation' ? ? 0.99021900 0.13951900 0.00000000 0.00000 -0.13951900 0.99021900 0.00000000 0.00000 0.00000000 -0.00000000 1.00000000 -9.32000 3 'helical symmetry operation' ? ? 0.99755200 0.06993100 0.00000000 0.00000 -0.06993100 0.99755200 0.00000000 0.00000 0.00000000 -0.00000000 1.00000000 -4.66000 4 'helical symmetry operation' ? ? 0.99755200 -0.06993100 0.00000000 0.00000 0.06993100 0.99755200 0.00000000 0.00000 -0.00000000 0.00000000 1.00000000 4.66000 5 'helical symmetry operation' ? ? -0.99021900 -0.13951900 0.00000000 0.00000 0.13951900 -0.99021900 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -9.32000 6 'helical symmetry operation' ? ? -0.99755200 -0.06993100 0.00000000 0.00000 0.06993100 -0.99755200 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -4.66000 7 'helical symmetry operation' ? ? -1.00000000 -0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 8 'helical symmetry operation' ? ? -0.99755200 0.06993100 0.00000000 0.00000 -0.06993100 -0.99755200 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 4.66000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A UQ4 1 C02 ? ? ? 1_555 A LEU 2 N ? ? A UQ4 1 A LEU 2 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale2 covale both ? B UQ4 1 C02 ? ? ? 1_555 B LEU 2 N ? ? B UQ4 1 B LEU 2 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale3 covale both ? C UQ4 1 C02 ? ? ? 1_555 C LEU 2 N ? ? C UQ4 1 C LEU 2 1_555 ? ? ? ? ? ? ? 1.328 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 UQ4 A 1 ? . . . . UQ4 A 1 ? 1_555 . . . . . . . ? 1 UQ4 None 'Non-standard residue' 2 UQ4 B 1 ? . . . . UQ4 B 1 ? 1_555 . . . . . . . ? 1 UQ4 None 'Non-standard residue' 3 UQ4 C 1 ? . . . . UQ4 C 1 ? 1_555 . . . . . . . ? 1 UQ4 None 'Non-standard residue' # _pdbx_entry_details.entry_id 9NEQ _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 Y _pdbx_entry_details.has_protein_modification Y # _pdbx_helical_symmetry.entry_id 9NEQ _pdbx_helical_symmetry.number_of_operations 8 _pdbx_helical_symmetry.rotation_per_n_subunits 4.01 _pdbx_helical_symmetry.rise_per_n_subunits 4.66 _pdbx_helical_symmetry.n_subunits_divisor 1 _pdbx_helical_symmetry.dyad_axis no _pdbx_helical_symmetry.circular_symmetry 2 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9NEQ _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 9NEQ _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 3.5 _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 881591 _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 7 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type COMPLEX _em_entity_assembly.name '(UQ4)LLLL(PTR)' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9NEQ _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 9NEQ _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 9NEQ _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _em_experiment.aggregation_state FILAMENT _em_experiment.entity_assembly_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A PTR 6 ? A PTR 6 2 1 Y 1 B PTR 6 ? B PTR 6 3 1 Y 1 C PTR 6 ? C PTR 6 # 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 LEU N N N N 1 LEU CA C N S 2 LEU C C N N 3 LEU O O N N 4 LEU CB C N N 5 LEU CG C N N 6 LEU CD1 C N N 7 LEU CD2 C N N 8 LEU OXT O N N 9 LEU H H N N 10 LEU H2 H N N 11 LEU HA H N N 12 LEU HB2 H N N 13 LEU HB3 H N N 14 LEU HG H N N 15 LEU HD11 H N N 16 LEU HD12 H N N 17 LEU HD13 H N N 18 LEU HD21 H N N 19 LEU HD22 H N N 20 LEU HD23 H N N 21 LEU HXT H N N 22 PTR N N N N 23 PTR CA C N S 24 PTR C C N N 25 PTR O O N N 26 PTR OXT O N N 27 PTR CB C N N 28 PTR CG C Y N 29 PTR CD1 C Y N 30 PTR CD2 C Y N 31 PTR CE1 C Y N 32 PTR CE2 C Y N 33 PTR CZ C Y N 34 PTR OH O N N 35 PTR P P N N 36 PTR O1P O N N 37 PTR O2P O N N 38 PTR O3P O N N 39 PTR H H N N 40 PTR H2 H N N 41 PTR HA H N N 42 PTR HXT H N N 43 PTR HB2 H N N 44 PTR HB3 H N N 45 PTR HD1 H N N 46 PTR HD2 H N N 47 PTR HE1 H N N 48 PTR HE2 H N N 49 PTR HO2P H N N 50 PTR HO3P H N N 51 UQ4 C02 C N N 52 UQ4 C50 C N N 53 UQ4 C51 C N N 54 UQ4 C53 C Y N 55 UQ4 C54 C Y N 56 UQ4 C55 C Y N 57 UQ4 C56 C Y N 58 UQ4 C60 C Y N 59 UQ4 C64 C Y N 60 UQ4 N52 N N N 61 UQ4 N57 N N N 62 UQ4 N61 N Y N 63 UQ4 N63 N Y N 64 UQ4 O01 O N N 65 UQ4 O58 O N N 66 UQ4 O59 O N N 67 UQ4 O62 O Y N 68 UQ4 H501 H N N 69 UQ4 H502 H N N 70 UQ4 H512 H N N 71 UQ4 H511 H N N 72 UQ4 H541 H N N 73 UQ4 H551 H N N 74 UQ4 H521 H N N 75 UQ4 OXT O N N 76 UQ4 HXT H N N 77 # 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 LEU N CA sing N N 1 LEU N H sing N N 2 LEU N H2 sing N N 3 LEU CA C sing N N 4 LEU CA CB sing N N 5 LEU CA HA sing N N 6 LEU C O doub N N 7 LEU C OXT sing N N 8 LEU CB CG sing N N 9 LEU CB HB2 sing N N 10 LEU CB HB3 sing N N 11 LEU CG CD1 sing N N 12 LEU CG CD2 sing N N 13 LEU CG HG sing N N 14 LEU CD1 HD11 sing N N 15 LEU CD1 HD12 sing N N 16 LEU CD1 HD13 sing N N 17 LEU CD2 HD21 sing N N 18 LEU CD2 HD22 sing N N 19 LEU CD2 HD23 sing N N 20 LEU OXT HXT sing N N 21 PTR N CA sing N N 22 PTR N H sing N N 23 PTR N H2 sing N N 24 PTR CA C sing N N 25 PTR CA CB sing N N 26 PTR CA HA sing N N 27 PTR C O doub N N 28 PTR C OXT sing N N 29 PTR OXT HXT sing N N 30 PTR CB CG sing N N 31 PTR CB HB2 sing N N 32 PTR CB HB3 sing N N 33 PTR CG CD1 doub Y N 34 PTR CG CD2 sing Y N 35 PTR CD1 CE1 sing Y N 36 PTR CD1 HD1 sing N N 37 PTR CD2 CE2 doub Y N 38 PTR CD2 HD2 sing N N 39 PTR CE1 CZ doub Y N 40 PTR CE1 HE1 sing N N 41 PTR CE2 CZ sing Y N 42 PTR CE2 HE2 sing N N 43 PTR CZ OH sing N N 44 PTR OH P sing N N 45 PTR P O1P doub N N 46 PTR P O2P sing N N 47 PTR P O3P sing N N 48 PTR O2P HO2P sing N N 49 PTR O3P HO3P sing N N 50 UQ4 C02 O01 doub N N 51 UQ4 C02 C50 sing N N 52 UQ4 C50 C51 sing N N 53 UQ4 C51 N52 sing N N 54 UQ4 C53 C64 sing Y N 55 UQ4 C53 N52 sing N N 56 UQ4 C53 C54 doub Y N 57 UQ4 C54 C55 sing Y N 58 UQ4 C55 C56 doub Y N 59 UQ4 C56 C60 sing Y N 60 UQ4 C56 N57 sing N N 61 UQ4 C60 N61 doub Y N 62 UQ4 C60 C64 sing Y N 63 UQ4 C64 N63 doub Y N 64 UQ4 N57 O58 doub N N 65 UQ4 N57 O59 sing N N 66 UQ4 N61 O62 sing Y N 67 UQ4 N63 O62 sing Y N 68 UQ4 C50 H501 sing N N 69 UQ4 C50 H502 sing N N 70 UQ4 C51 H512 sing N N 71 UQ4 C51 H511 sing N N 72 UQ4 C54 H541 sing N N 73 UQ4 C55 H551 sing N N 74 UQ4 N52 H521 sing N N 75 UQ4 C02 OXT sing N N 76 UQ4 OXT HXT sing N N 77 # _em_admin.current_status REL _em_admin.deposition_date 2025-02-20 _em_admin.deposition_site RCSB _em_admin.entry_id 9NEQ _em_admin.last_update 2026-03-11 _em_admin.map_release_date 2026-03-11 _em_admin.title 'Cryo-EM of NBD-L4pY nanofibers at 1.25mM concentration' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 32630 _em_entity_assembly_naturalsource.organism 'synthetic construct' _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 C2 _em_helical_entity.angular_rotation_per_subunit 4.01 _em_helical_entity.axial_rise_per_subunit 4.66 # _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 50 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'MODEL REFINEMENT' ? 2 ? ? ? PHENIX 1.18.2_3874 'IMAGE ACQUISITION' ? 3 ? ? 1 ? ? MASKING ? 4 ? ? ? ? ? 'CTF CORRECTION' ? 5 1 ? ? ? ? 'LAYERLINE INDEXING' ? 6 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 7 ? ? ? ? ? 'MODEL FITTING' ? 8 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? # _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 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' GM138756 1 'National Institutes of Health/National Cancer Institute (NIH/NCI)' 'United States' CA142746 2 # _atom_sites.entry_id 9NEQ _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 # loop_ #