data_9PEK # _entry.id 9PEK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.416 _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 9PEK pdb_00009pek 10.2210/pdb9pek/pdb WWPDB D_1000297674 ? ? EMDB EMD-71565 ? ? # 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 2026-07-22 ? 2 'EM metadata' 1 0 2026-07-22 ? 3 'Additional map' 1 0 2026-07-22 1 4 'Half map' 1 0 2026-07-22 1 5 'Half map' 1 0 2026-07-22 2 6 Image 1 0 2026-07-22 ? 7 'Primary map' 1 0 2026-07-22 ? # 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 'Additional map' repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 'Half map' repository 'Initial release' ? ? 6 6 Image repository 'Initial release' ? ? 7 7 'Primary map' repository 'Initial release' ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9PEK _pdbx_database_status.recvd_initial_deposition_date 2025-07-02 _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 'QFX11 peptide nanofibril' _pdbx_database_related.db_id EMD-71565 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email ehe2n@virginia.edu _pdbx_contact_author.name_first Edward _pdbx_contact_author.name_last Egelman _pdbx_contact_author.name_mi H. _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4844-5212 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Sonani, R.R.' 1 ? 'Schremmer, Z.P.' 2 ? 'Nilsson, B.L.' 3 ? 'Egelman, E.H.' 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 'QFX11 peptide nanofibril' _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 'Sonani, R.R.' 1 ? primary 'Egelman, E.H.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'QFX11 peptide' _entity.formula_weight 1531.730 _entity.pdbx_number_of_molecules 4 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 '(ACE)QEFKFQFEFKQ(NH2)' _entity_poly.pdbx_seq_one_letter_code_can XQEFKFQFEFKQX _entity_poly.pdbx_strand_id D,E,I,J _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 ACE n 1 2 GLN n 1 3 GLU n 1 4 PHE n 1 5 LYS n 1 6 PHE n 1 7 GLN n 1 8 PHE n 1 9 GLU n 1 10 PHE n 1 11 LYS n 1 12 GLN n 1 13 NH2 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 13 _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 ACE non-polymer . 'ACETYL GROUP' ? 'C2 H4 O' 44.053 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 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 # 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 ACE 1 0 0 ACE ACE D . n A 1 2 GLN 2 1 1 GLN GLN D . n A 1 3 GLU 3 2 2 GLU GLU D . n A 1 4 PHE 4 3 3 PHE PHE D . n A 1 5 LYS 5 4 4 LYS LYS D . n A 1 6 PHE 6 5 5 PHE PHE D . n A 1 7 GLN 7 6 6 GLN GLN D . n A 1 8 PHE 8 7 7 PHE PHE D . n A 1 9 GLU 9 8 8 GLU GLU D . n A 1 10 PHE 10 9 9 PHE PHE D . n A 1 11 LYS 11 10 10 LYS LYS D . n A 1 12 GLN 12 11 11 GLN GLN D . n A 1 13 NH2 13 12 12 NH2 NH2 D . n B 1 1 ACE 1 0 0 ACE ACE E . n B 1 2 GLN 2 1 1 GLN GLN E . n B 1 3 GLU 3 2 2 GLU GLU E . n B 1 4 PHE 4 3 3 PHE PHE E . n B 1 5 LYS 5 4 4 LYS LYS E . n B 1 6 PHE 6 5 5 PHE PHE E . n B 1 7 GLN 7 6 6 GLN GLN E . n B 1 8 PHE 8 7 7 PHE PHE E . n B 1 9 GLU 9 8 8 GLU GLU E . n B 1 10 PHE 10 9 9 PHE PHE E . n B 1 11 LYS 11 10 10 LYS LYS E . n B 1 12 GLN 12 11 11 GLN GLN E . n B 1 13 NH2 13 12 12 NH2 NH2 E . n C 1 1 ACE 1 0 0 ACE ACE I . n C 1 2 GLN 2 1 1 GLN GLN I . n C 1 3 GLU 3 2 2 GLU GLU I . n C 1 4 PHE 4 3 3 PHE PHE I . n C 1 5 LYS 5 4 4 LYS LYS I . n C 1 6 PHE 6 5 5 PHE PHE I . n C 1 7 GLN 7 6 6 GLN GLN I . n C 1 8 PHE 8 7 7 PHE PHE I . n C 1 9 GLU 9 8 8 GLU GLU I . n C 1 10 PHE 10 9 9 PHE PHE I . n C 1 11 LYS 11 10 10 LYS LYS I . n C 1 12 GLN 12 11 11 GLN GLN I . n C 1 13 NH2 13 12 12 NH2 NH2 I . n D 1 1 ACE 1 0 0 ACE ACE J . n D 1 2 GLN 2 1 1 GLN GLN J . n D 1 3 GLU 3 2 2 GLU GLU J . n D 1 4 PHE 4 3 3 PHE PHE J . n D 1 5 LYS 5 4 4 LYS LYS J . n D 1 6 PHE 6 5 5 PHE PHE J . n D 1 7 GLN 7 6 6 GLN GLN J . n D 1 8 PHE 8 7 7 PHE PHE J . n D 1 9 GLU 9 8 8 GLU GLU J . n D 1 10 PHE 10 9 9 PHE PHE J . n D 1 11 LYS 11 10 10 LYS LYS J . n D 1 12 GLN 12 11 11 GLN GLN J . n D 1 13 NH2 13 12 12 NH2 NH2 J . n # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 9PEK _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 9PEK _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 9PEK _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 9PEK _refine.pdbx_diffrn_id ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high . _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_Zscore _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.006 ? 456 ? f_bond_d ? ? ? 'ELECTRON MICROSCOPY' ? 1.172 ? 596 ? f_angle_d ? ? ? 'ELECTRON MICROSCOPY' ? 26.565 ? 48 ? f_dihedral_angle_d ? ? ? 'ELECTRON MICROSCOPY' ? 0.030 ? 44 ? f_chiral_restr ? ? ? 'ELECTRON MICROSCOPY' ? 0.001 ? 84 ? f_plane_restr ? ? ? # _struct.entry_id 9PEK _struct.title 'QFX11 peptide nanofibril' _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 9PEK _struct_keywords.text 'Short peptide, Cross beta, Nanofibril, 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 1 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9PEK _struct_ref.pdbx_db_accession 9PEK _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 9PEK D 1 ? 13 ? 9PEK 0 ? 12 ? 0 12 2 1 9PEK E 1 ? 13 ? 9PEK 0 ? 12 ? 0 12 3 1 9PEK I 1 ? 13 ? 9PEK 0 ? 12 ? 0 12 4 1 9PEK J 1 ? 13 ? 9PEK 0 ? 12 ? 0 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list 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' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_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 ACE 1 C ? ? ? 1_555 A GLN 2 N ? ? D ACE 0 D GLN 1 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale2 covale both ? A GLN 12 C ? ? ? 1_555 A NH2 13 N ? ? D GLN 11 D NH2 12 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale3 covale both ? B ACE 1 C ? ? ? 1_555 B GLN 2 N ? ? E ACE 0 E GLN 1 1_555 ? ? ? ? ? ? ? 1.344 ? ? covale4 covale both ? B GLN 12 C ? ? ? 1_555 B NH2 13 N ? ? E GLN 11 E NH2 12 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale5 covale both ? C ACE 1 C ? ? ? 1_555 C GLN 2 N ? ? I ACE 0 I GLN 1 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale6 covale both ? C GLN 12 C ? ? ? 1_555 C NH2 13 N ? ? I GLN 11 I NH2 12 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale7 covale both ? D ACE 1 C ? ? ? 1_555 D GLN 2 N ? ? J ACE 0 J GLN 1 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale8 covale both ? D GLN 12 C ? ? ? 1_555 D NH2 13 N ? ? J GLN 11 J NH2 12 1_555 ? ? ? ? ? ? ? 1.329 ? ? # _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 ACE A 1 ? GLN A 2 ? ACE D 0 ? 1_555 GLN D 1 ? 1_555 . . GLN 18 ACE None 'Terminal acetylation' 2 ACE B 1 ? GLN B 2 ? ACE E 0 ? 1_555 GLN E 1 ? 1_555 . . GLN 18 ACE None 'Terminal acetylation' 3 ACE C 1 ? GLN C 2 ? ACE I 0 ? 1_555 GLN I 1 ? 1_555 . . GLN 18 ACE None 'Terminal acetylation' 4 ACE D 1 ? GLN D 2 ? ACE J 0 ? 1_555 GLN J 1 ? 1_555 . . GLN 18 ACE None 'Terminal acetylation' 5 NH2 A 13 ? GLN A 12 ? NH2 D 12 ? 1_555 GLN D 11 ? 1_555 . . GLN 18 NH2 None 'Terminal amidation' 6 NH2 B 13 ? GLN B 12 ? NH2 E 12 ? 1_555 GLN E 11 ? 1_555 . . GLN 18 NH2 None 'Terminal amidation' 7 NH2 C 13 ? GLN C 12 ? NH2 I 12 ? 1_555 GLN I 11 ? 1_555 . . GLN 18 NH2 None 'Terminal amidation' 8 NH2 D 13 ? GLN D 12 ? NH2 J 12 ? 1_555 GLN J 11 ? 1_555 . . GLN 18 NH2 None 'Terminal amidation' # _pdbx_entry_details.entry_id 9PEK _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 N _pdbx_entry_details.has_protein_modification Y # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id LYS _pdbx_validate_torsion.auth_asym_id D _pdbx_validate_torsion.auth_seq_id 10 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 54.81 _pdbx_validate_torsion.psi -166.51 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9PEK _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 9PEK _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 4.1 _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 14184 _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 RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'Helical oligomer of QFX11 peptides' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9PEK _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 1200 _em_imaging.nominal_defocus_max 2400 _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 9PEK _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 9PEK _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _em_experiment.aggregation_state 'HELICAL ARRAY' _em_experiment.entity_assembly_id 1 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ACE C C N N 1 ACE O O N N 2 ACE CH3 C N N 3 ACE H H N N 4 ACE H1 H N N 5 ACE H2 H N N 6 ACE H3 H N N 7 GLN N N N N 8 GLN CA C N S 9 GLN C C N N 10 GLN O O N N 11 GLN CB C N N 12 GLN CG C N N 13 GLN CD C N N 14 GLN OE1 O N N 15 GLN NE2 N N N 16 GLN OXT O N N 17 GLN H H N N 18 GLN H2 H N N 19 GLN HA H N N 20 GLN HB2 H N N 21 GLN HB3 H N N 22 GLN HG2 H N N 23 GLN HG3 H N N 24 GLN HE21 H N N 25 GLN HE22 H N N 26 GLN HXT H N N 27 GLU N N N N 28 GLU CA C N S 29 GLU C C N N 30 GLU O O N N 31 GLU CB C N N 32 GLU CG C N N 33 GLU CD C N N 34 GLU OE1 O N N 35 GLU OE2 O N N 36 GLU OXT O N N 37 GLU H H N N 38 GLU H2 H N N 39 GLU HA H N N 40 GLU HB2 H N N 41 GLU HB3 H N N 42 GLU HG2 H N N 43 GLU HG3 H N N 44 GLU HE2 H N N 45 GLU HXT H N N 46 LYS N N N N 47 LYS CA C N S 48 LYS C C N N 49 LYS O O N N 50 LYS CB C N N 51 LYS CG C N N 52 LYS CD C N N 53 LYS CE C N N 54 LYS NZ N N N 55 LYS OXT O N N 56 LYS H H N N 57 LYS H2 H N N 58 LYS HA H N N 59 LYS HB2 H N N 60 LYS HB3 H N N 61 LYS HG2 H N N 62 LYS HG3 H N N 63 LYS HD2 H N N 64 LYS HD3 H N N 65 LYS HE2 H N N 66 LYS HE3 H N N 67 LYS HZ1 H N N 68 LYS HZ2 H N N 69 LYS HZ3 H N N 70 LYS HXT H N N 71 NH2 N N N N 72 NH2 HN1 H N N 73 NH2 HN2 H N N 74 PHE N N N N 75 PHE CA C N S 76 PHE C C N N 77 PHE O O N N 78 PHE CB C N N 79 PHE CG C Y N 80 PHE CD1 C Y N 81 PHE CD2 C Y N 82 PHE CE1 C Y N 83 PHE CE2 C Y N 84 PHE CZ C Y N 85 PHE OXT O N N 86 PHE H H N N 87 PHE H2 H N N 88 PHE HA H N N 89 PHE HB2 H N N 90 PHE HB3 H N N 91 PHE HD1 H N N 92 PHE HD2 H N N 93 PHE HE1 H N N 94 PHE HE2 H N N 95 PHE HZ H N N 96 PHE HXT H N N 97 # 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 ACE C O doub N N 1 ACE C CH3 sing N N 2 ACE C H sing N N 3 ACE CH3 H1 sing N N 4 ACE CH3 H2 sing N N 5 ACE CH3 H3 sing N N 6 GLN N CA sing N N 7 GLN N H sing N N 8 GLN N H2 sing N N 9 GLN CA C sing N N 10 GLN CA CB sing N N 11 GLN CA HA sing N N 12 GLN C O doub N N 13 GLN C OXT sing N N 14 GLN CB CG sing N N 15 GLN CB HB2 sing N N 16 GLN CB HB3 sing N N 17 GLN CG CD sing N N 18 GLN CG HG2 sing N N 19 GLN CG HG3 sing N N 20 GLN CD OE1 doub N N 21 GLN CD NE2 sing N N 22 GLN NE2 HE21 sing N N 23 GLN NE2 HE22 sing N N 24 GLN OXT HXT sing N N 25 GLU N CA sing N N 26 GLU N H sing N N 27 GLU N H2 sing N N 28 GLU CA C sing N N 29 GLU CA CB sing N N 30 GLU CA HA sing N N 31 GLU C O doub N N 32 GLU C OXT sing N N 33 GLU CB CG sing N N 34 GLU CB HB2 sing N N 35 GLU CB HB3 sing N N 36 GLU CG CD sing N N 37 GLU CG HG2 sing N N 38 GLU CG HG3 sing N N 39 GLU CD OE1 doub N N 40 GLU CD OE2 sing N N 41 GLU OE2 HE2 sing N N 42 GLU OXT HXT sing N N 43 LYS N CA sing N N 44 LYS N H sing N N 45 LYS N H2 sing N N 46 LYS CA C sing N N 47 LYS CA CB sing N N 48 LYS CA HA sing N N 49 LYS C O doub N N 50 LYS C OXT sing N N 51 LYS CB CG sing N N 52 LYS CB HB2 sing N N 53 LYS CB HB3 sing N N 54 LYS CG CD sing N N 55 LYS CG HG2 sing N N 56 LYS CG HG3 sing N N 57 LYS CD CE sing N N 58 LYS CD HD2 sing N N 59 LYS CD HD3 sing N N 60 LYS CE NZ sing N N 61 LYS CE HE2 sing N N 62 LYS CE HE3 sing N N 63 LYS NZ HZ1 sing N N 64 LYS NZ HZ2 sing N N 65 LYS NZ HZ3 sing N N 66 LYS OXT HXT sing N N 67 NH2 N HN1 sing N N 68 NH2 N HN2 sing N N 69 PHE N CA sing N N 70 PHE N H sing N N 71 PHE N H2 sing N N 72 PHE CA C sing N N 73 PHE CA CB sing N N 74 PHE CA HA sing N N 75 PHE C O doub N N 76 PHE C OXT sing N N 77 PHE CB CG sing N N 78 PHE CB HB2 sing N N 79 PHE CB HB3 sing N N 80 PHE CG CD1 doub Y N 81 PHE CG CD2 sing Y N 82 PHE CD1 CE1 sing Y N 83 PHE CD1 HD1 sing N N 84 PHE CD2 CE2 doub Y N 85 PHE CD2 HD2 sing N N 86 PHE CE1 CZ doub Y N 87 PHE CE1 HE1 sing N N 88 PHE CE2 CZ sing Y N 89 PHE CE2 HE2 sing N N 90 PHE CZ HZ sing N N 91 PHE OXT HXT sing N N 92 # _em_admin.current_status REL _em_admin.deposition_date 2025-07-02 _em_admin.deposition_site RCSB _em_admin.entry_id 9PEK _em_admin.last_update 2026-07-22 _em_admin.map_release_date 2026-07-22 _em_admin.title 'QFX11 peptide nanofibril' # _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_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 32630 _em_entity_assembly_recombinant.organism 'synthetic construct' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.details ? _em_helical_entity.axial_symmetry C2 _em_helical_entity.angular_rotation_per_subunit -4.5 _em_helical_entity.axial_rise_per_subunit 4.7 # _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 _em_software.reference_DOI 'PARTICLE SELECTION' ? 1 1 ? ? cryoSPARC ? ? 'MODEL REFINEMENT' ? 2 ? ? ? PHENIX 1.20.1_4487: ? 'IMAGE ACQUISITION' ? 3 1 1 1 ? ? ? MASKING ? 4 1 1 1 ? ? ? 'CTF CORRECTION' ? 5 1 ? ? ? ? ? 'LAYERLINE INDEXING' ? 6 1 1 1 ? ? ? 'DIFFRACTION INDEXING' ? 7 1 1 1 ? ? ? 'MODEL FITTING' ? 8 1 1 1 ? ? ? OTHER ? 9 1 1 1 ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? ? RECONSTRUCTION ? 13 1 ? ? cryoSPARC ? ? # _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 Science Foundation (NSF, United States)' 'United States' 'NSF 2304854' 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' GM122510 2 # _atom_sites.entry_id 9PEK _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_ #