data_9Y1V # _entry.id 9Y1V # _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 9Y1V pdb_00009y1v 10.2210/pdb9y1v/pdb WWPDB D_1000299723 ? ? EMDB EMD-72404 ? ? # 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 2026-09-09 ? 2 'EM metadata' 1 0 2026-09-09 ? # 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' ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9Y1V _pdbx_database_status.recvd_initial_deposition_date 2025-08-31 _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 structure of designed Orb2 amyloid (FIMMF, polymorph 2)' _pdbx_database_related.db_id EMD-72404 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email lukasz.joachimiak@utsouthwestern.edu _pdbx_contact_author.name_first Lukasz _pdbx_contact_author.name_last Joachimiak _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-3061-5850 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Singh, R.' 1 0000-0003-2456-7127 'Kaili, L.' 2 ? 'Si, K.' 3 0000-0002-9613-6273 'Joachimiak, L.' 4 0000-0003-3061-5850 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Cryo-EM structure of designed Orb2 amyloid (FIMMF, polymorph 2)' _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 'Singh, R.' 1 0000-0003-2456-7127 primary 'Kaili, L.' 2 ? primary 'Si, K.' 3 0000-0002-9613-6273 primary 'Joachimiak, L.' 4 0000-0003-3061-5850 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Translational regulator orb2' _entity.formula_weight 4018.394 _entity.pdbx_number_of_molecules 3 _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 no _entity_poly.pdbx_seq_one_letter_code QLHQQQHQQQHFQHIQHMQQMQFHQHQQQLS _entity_poly.pdbx_seq_one_letter_code_can QLHQQQHQQQHFQHIQHMQQMQFHQHQQQLS _entity_poly.pdbx_strand_id A,B,C _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 GLN n 1 2 LEU n 1 3 HIS n 1 4 GLN n 1 5 GLN n 1 6 GLN n 1 7 HIS n 1 8 GLN n 1 9 GLN n 1 10 GLN n 1 11 HIS n 1 12 PHE n 1 13 GLN n 1 14 HIS n 1 15 ILE n 1 16 GLN n 1 17 HIS n 1 18 MET n 1 19 GLN n 1 20 GLN n 1 21 MET n 1 22 GLN n 1 23 PHE n 1 24 HIS n 1 25 GLN n 1 26 HIS n 1 27 GLN n 1 28 GLN n 1 29 GLN n 1 30 LEU n 1 31 SER 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 31 _pdbx_entity_src_syn.organism_scientific 'Drosophila melanogaster' _pdbx_entity_src_syn.organism_common_name 'fruit fly' _pdbx_entity_src_syn.ncbi_taxonomy_id 7227 _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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # 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 GLN 1 1 1 GLN GLN A . n A 1 2 LEU 2 2 2 LEU LEU A . n A 1 3 HIS 3 3 3 HIS HIS A . n A 1 4 GLN 4 4 4 GLN GLN A . n A 1 5 GLN 5 5 5 GLN GLN A . n A 1 6 GLN 6 6 6 GLN GLN A . n A 1 7 HIS 7 7 7 HIS HIS A . n A 1 8 GLN 8 8 8 GLN GLN A . n A 1 9 GLN 9 9 9 GLN GLN A . n A 1 10 GLN 10 10 10 GLN GLN A . n A 1 11 HIS 11 11 11 HIS HIS A . n A 1 12 PHE 12 12 12 PHE PHE A . n A 1 13 GLN 13 13 13 GLN GLN A . n A 1 14 HIS 14 14 14 HIS HIS A . n A 1 15 ILE 15 15 15 ILE ILE A . n A 1 16 GLN 16 16 16 GLN GLN A . n A 1 17 HIS 17 17 17 HIS HIS A . n A 1 18 MET 18 18 18 MET MET A . n A 1 19 GLN 19 19 19 GLN GLN A . n A 1 20 GLN 20 20 20 GLN GLN A . n A 1 21 MET 21 21 21 MET MET A . n A 1 22 GLN 22 22 22 GLN GLN A . n A 1 23 PHE 23 23 23 PHE PHE A . n A 1 24 HIS 24 24 24 HIS HIS A . n A 1 25 GLN 25 25 25 GLN GLN A . n A 1 26 HIS 26 26 26 HIS HIS A . n A 1 27 GLN 27 27 27 GLN GLN A . n A 1 28 GLN 28 28 28 GLN GLN A . n A 1 29 GLN 29 29 29 GLN GLN A . n A 1 30 LEU 30 30 30 LEU LEU A . n A 1 31 SER 31 31 31 SER SER A . n B 1 1 GLN 1 1 1 GLN GLN B . n B 1 2 LEU 2 2 2 LEU LEU B . n B 1 3 HIS 3 3 3 HIS HIS B . n B 1 4 GLN 4 4 4 GLN GLN B . n B 1 5 GLN 5 5 5 GLN GLN B . n B 1 6 GLN 6 6 6 GLN GLN B . n B 1 7 HIS 7 7 7 HIS HIS B . n B 1 8 GLN 8 8 8 GLN GLN B . n B 1 9 GLN 9 9 9 GLN GLN B . n B 1 10 GLN 10 10 10 GLN GLN B . n B 1 11 HIS 11 11 11 HIS HIS B . n B 1 12 PHE 12 12 12 PHE PHE B . n B 1 13 GLN 13 13 13 GLN GLN B . n B 1 14 HIS 14 14 14 HIS HIS B . n B 1 15 ILE 15 15 15 ILE ILE B . n B 1 16 GLN 16 16 16 GLN GLN B . n B 1 17 HIS 17 17 17 HIS HIS B . n B 1 18 MET 18 18 18 MET MET B . n B 1 19 GLN 19 19 19 GLN GLN B . n B 1 20 GLN 20 20 20 GLN GLN B . n B 1 21 MET 21 21 21 MET MET B . n B 1 22 GLN 22 22 22 GLN GLN B . n B 1 23 PHE 23 23 23 PHE PHE B . n B 1 24 HIS 24 24 24 HIS HIS B . n B 1 25 GLN 25 25 25 GLN GLN B . n B 1 26 HIS 26 26 26 HIS HIS B . n B 1 27 GLN 27 27 27 GLN GLN B . n B 1 28 GLN 28 28 28 GLN GLN B . n B 1 29 GLN 29 29 29 GLN GLN B . n B 1 30 LEU 30 30 30 LEU LEU B . n B 1 31 SER 31 31 31 SER SER B . n C 1 1 GLN 1 1 1 GLN GLN C . n C 1 2 LEU 2 2 2 LEU LEU C . n C 1 3 HIS 3 3 3 HIS HIS C . n C 1 4 GLN 4 4 4 GLN GLN C . n C 1 5 GLN 5 5 5 GLN GLN C . n C 1 6 GLN 6 6 6 GLN GLN C . n C 1 7 HIS 7 7 7 HIS HIS C . n C 1 8 GLN 8 8 8 GLN GLN C . n C 1 9 GLN 9 9 9 GLN GLN C . n C 1 10 GLN 10 10 10 GLN GLN C . n C 1 11 HIS 11 11 11 HIS HIS C . n C 1 12 PHE 12 12 12 PHE PHE C . n C 1 13 GLN 13 13 13 GLN GLN C . n C 1 14 HIS 14 14 14 HIS HIS C . n C 1 15 ILE 15 15 15 ILE ILE C . n C 1 16 GLN 16 16 16 GLN GLN C . n C 1 17 HIS 17 17 17 HIS HIS C . n C 1 18 MET 18 18 18 MET MET C . n C 1 19 GLN 19 19 19 GLN GLN C . n C 1 20 GLN 20 20 20 GLN GLN C . n C 1 21 MET 21 21 21 MET MET C . n C 1 22 GLN 22 22 22 GLN GLN C . n C 1 23 PHE 23 23 23 PHE PHE C . n C 1 24 HIS 24 24 24 HIS HIS C . n C 1 25 GLN 25 25 25 GLN GLN C . n C 1 26 HIS 26 26 26 HIS HIS C . n C 1 27 GLN 27 27 27 GLN GLN C . n C 1 28 GLN 28 28 28 GLN GLN C . n C 1 29 GLN 29 29 29 GLN GLN C . n C 1 30 LEU 30 30 30 LEU LEU C . n C 1 31 SER 31 31 31 SER SER C . n # _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 9Y1V _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 9Y1V _struct.title 'Cryo-EM structure of designed Orb2 amyloid (FIMMF, polymorph 2)' _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 9Y1V _struct_keywords.text 'Polymorph 2, Recombinant Protein, Orb2 Amyloid Core, Designed Mutants, 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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code ORB2_DROME _struct_ref.pdbx_db_accession Q9VSR3 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code QLHQQQHQQQHQQHQQHQQQQQLHQHQQQLS _struct_ref.pdbx_align_begin 176 # 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 9Y1V A 1 ? 31 ? Q9VSR3 176 ? 206 ? 1 31 2 1 9Y1V B 1 ? 31 ? Q9VSR3 176 ? 206 ? 1 31 3 1 9Y1V C 1 ? 31 ? Q9VSR3 176 ? 206 ? 1 31 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 9Y1V PHE A 12 ? UNP Q9VSR3 GLN 187 'engineered mutation' 12 1 1 9Y1V ILE A 15 ? UNP Q9VSR3 GLN 190 'engineered mutation' 15 2 1 9Y1V MET A 18 ? UNP Q9VSR3 GLN 193 'engineered mutation' 18 3 1 9Y1V MET A 21 ? UNP Q9VSR3 GLN 196 'engineered mutation' 21 4 1 9Y1V PHE A 23 ? UNP Q9VSR3 LEU 198 'engineered mutation' 23 5 2 9Y1V PHE B 12 ? UNP Q9VSR3 GLN 187 'engineered mutation' 12 6 2 9Y1V ILE B 15 ? UNP Q9VSR3 GLN 190 'engineered mutation' 15 7 2 9Y1V MET B 18 ? UNP Q9VSR3 GLN 193 'engineered mutation' 18 8 2 9Y1V MET B 21 ? UNP Q9VSR3 GLN 196 'engineered mutation' 21 9 2 9Y1V PHE B 23 ? UNP Q9VSR3 LEU 198 'engineered mutation' 23 10 3 9Y1V PHE C 12 ? UNP Q9VSR3 GLN 187 'engineered mutation' 12 11 3 9Y1V ILE C 15 ? UNP Q9VSR3 GLN 190 'engineered mutation' 15 12 3 9Y1V MET C 18 ? UNP Q9VSR3 GLN 193 'engineered mutation' 18 13 3 9Y1V MET C 21 ? UNP Q9VSR3 GLN 196 'engineered mutation' 21 14 3 9Y1V PHE C 23 ? UNP Q9VSR3 LEU 198 'engineered mutation' 23 15 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 3 ? AA3 ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? parallel AA1 2 3 ? parallel AA2 1 2 ? parallel AA2 2 3 ? parallel AA3 1 2 ? parallel AA3 2 3 ? parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 LEU A 2 ? GLN A 5 ? LEU A 2 GLN A 5 AA1 2 LEU B 2 ? GLN B 5 ? LEU B 2 GLN B 5 AA1 3 LEU C 2 ? GLN C 5 ? LEU C 2 GLN C 5 AA2 1 HIS A 17 ? GLN A 20 ? HIS A 17 GLN A 20 AA2 2 HIS B 17 ? GLN B 20 ? HIS B 17 GLN B 20 AA2 3 HIS C 17 ? GLN C 20 ? HIS C 17 GLN C 20 AA3 1 GLN A 29 ? LEU A 30 ? GLN A 29 LEU A 30 AA3 2 GLN B 29 ? LEU B 30 ? GLN B 29 LEU B 30 AA3 3 GLN C 29 ? LEU C 30 ? GLN C 29 LEU C 30 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N HIS A 3 ? N HIS A 3 O LEU B 2 ? O LEU B 2 AA1 2 3 N HIS B 3 ? N HIS B 3 O LEU C 2 ? O LEU C 2 AA2 1 2 N HIS A 17 ? N HIS A 17 O MET B 18 ? O MET B 18 AA2 2 3 N HIS B 17 ? N HIS B 17 O MET C 18 ? O MET C 18 AA3 1 2 N LEU A 30 ? N LEU A 30 O GLN B 29 ? O GLN B 29 AA3 2 3 N LEU B 30 ? N LEU B 30 O GLN C 29 ? O GLN C 29 # _pdbx_entry_details.entry_id 9Y1V _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PHE A 23 ? ? -100.71 74.82 2 1 PHE B 23 ? ? -100.73 74.81 3 1 PHE C 23 ? ? -100.69 74.74 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9Y1V _em_3d_fitting.method ? _em_3d_fitting.target_criteria 'Cross Correlation Coefficient' _em_3d_fitting.details 'Initial model fitting was performed using Coot and Phenix, with final adjustments completed in ChimeraX.' _em_3d_fitting.overall_b_value 846 _em_3d_fitting.ref_space REAL _em_3d_fitting.ref_protocol 'AB INITIO MODEL' # _em_3d_fitting_list.id 1 _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.pdb_entry_id . _em_3d_fitting_list.pdb_chain_id . _em_3d_fitting_list.pdb_chain_residue_range . _em_3d_fitting_list.details 'Initial model generated using ModelAngelo from the cryo-EM map.' _em_3d_fitting_list.chain_id ? _em_3d_fitting_list.chain_residue_range ? _em_3d_fitting_list.source_name Other _em_3d_fitting_list.type 'in silico model' _em_3d_fitting_list.accession_code ? _em_3d_fitting_list.initial_refinement_model_id ? # _em_3d_reconstruction.entry_id 9Y1V _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm 'FOURIER SPACE' _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 3.4 _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 451817 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages 1 _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details '10mM HEPES, 75Mm NaCl, 2% glycerol, 2mM MgCl2, 10mM KCl' _em_buffer.pH 7.15 # _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 'Cryo-EM Structure of designed Orb2 amyloid (FIMMF; Polymorph 2)' _em_entity_assembly.details 'Orb2 Amyloid Peptide are chemically synthesized' _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9Y1V _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 'FEI TITAN KRIOS AUTOGRID HOLDER' _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 2.7 _em_imaging.nominal_defocus_min 1000 _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 50 _em_imaging.specimen_id 1 _em_imaging.cryogen NITROGEN _em_imaging.objective_aperture ? _em_imaging.microscope_serial_number ? _em_imaging.microscope_version ? # _em_sample_support.id 1 _em_sample_support.film_material ? _em_sample_support.method ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'Quantifoil R1.2/1.3' _em_sample_support.details ? _em_sample_support.specimen_id 1 _em_sample_support.citation_id ? # _em_vitrification.entry_id 9Y1V _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 95 _em_vitrification.temp ? _em_vitrification.chamber_temperature 291.15 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details 'Vitrification Carried out in liquid Nitrogen atmosphere' # _em_experiment.entry_id 9Y1V _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state FILAMENT _em_experiment.entity_assembly_id 1 # _em_single_particle_entity.entry_id 9Y1V _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry C1 # 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 GLN N N N N 1 GLN CA C N S 2 GLN C C N N 3 GLN O O N N 4 GLN CB C N N 5 GLN CG C N N 6 GLN CD C N N 7 GLN OE1 O N N 8 GLN NE2 N N N 9 GLN OXT O N N 10 GLN H H N N 11 GLN H2 H N N 12 GLN HA H N N 13 GLN HB2 H N N 14 GLN HB3 H N N 15 GLN HG2 H N N 16 GLN HG3 H N N 17 GLN HE21 H N N 18 GLN HE22 H N N 19 GLN HXT H N N 20 HIS N N N N 21 HIS CA C N S 22 HIS C C N N 23 HIS O O N N 24 HIS CB C N N 25 HIS CG C Y N 26 HIS ND1 N Y N 27 HIS CD2 C Y N 28 HIS CE1 C Y N 29 HIS NE2 N Y N 30 HIS OXT O N N 31 HIS H H N N 32 HIS H2 H N N 33 HIS HA H N N 34 HIS HB2 H N N 35 HIS HB3 H N N 36 HIS HD1 H N N 37 HIS HD2 H N N 38 HIS HE1 H N N 39 HIS HE2 H N N 40 HIS HXT H N N 41 ILE N N N N 42 ILE CA C N S 43 ILE C C N N 44 ILE O O N N 45 ILE CB C N S 46 ILE CG1 C N N 47 ILE CG2 C N N 48 ILE CD1 C N N 49 ILE OXT O N N 50 ILE H H N N 51 ILE H2 H N N 52 ILE HA H N N 53 ILE HB H N N 54 ILE HG12 H N N 55 ILE HG13 H N N 56 ILE HG21 H N N 57 ILE HG22 H N N 58 ILE HG23 H N N 59 ILE HD11 H N N 60 ILE HD12 H N N 61 ILE HD13 H N N 62 ILE HXT H N N 63 LEU N N N N 64 LEU CA C N S 65 LEU C C N N 66 LEU O O N N 67 LEU CB C N N 68 LEU CG C N N 69 LEU CD1 C N N 70 LEU CD2 C N N 71 LEU OXT O N N 72 LEU H H N N 73 LEU H2 H N N 74 LEU HA H N N 75 LEU HB2 H N N 76 LEU HB3 H N N 77 LEU HG H N N 78 LEU HD11 H N N 79 LEU HD12 H N N 80 LEU HD13 H N N 81 LEU HD21 H N N 82 LEU HD22 H N N 83 LEU HD23 H N N 84 LEU HXT H N N 85 MET N N N N 86 MET CA C N S 87 MET C C N N 88 MET O O N N 89 MET CB C N N 90 MET CG C N N 91 MET SD S N N 92 MET CE C N N 93 MET OXT O N N 94 MET H H N N 95 MET H2 H N N 96 MET HA H N N 97 MET HB2 H N N 98 MET HB3 H N N 99 MET HG2 H N N 100 MET HG3 H N N 101 MET HE1 H N N 102 MET HE2 H N N 103 MET HE3 H N N 104 MET HXT H N N 105 PHE N N N N 106 PHE CA C N S 107 PHE C C N N 108 PHE O O N N 109 PHE CB C N N 110 PHE CG C Y N 111 PHE CD1 C Y N 112 PHE CD2 C Y N 113 PHE CE1 C Y N 114 PHE CE2 C Y N 115 PHE CZ C Y N 116 PHE OXT O N N 117 PHE H H N N 118 PHE H2 H N N 119 PHE HA H N N 120 PHE HB2 H N N 121 PHE HB3 H N N 122 PHE HD1 H N N 123 PHE HD2 H N N 124 PHE HE1 H N N 125 PHE HE2 H N N 126 PHE HZ H N N 127 PHE HXT H N N 128 SER N N N N 129 SER CA C N S 130 SER C C N N 131 SER O O N N 132 SER CB C N N 133 SER OG O N N 134 SER OXT O N N 135 SER H H N N 136 SER H2 H N N 137 SER HA H N N 138 SER HB2 H N N 139 SER HB3 H N N 140 SER HG H N N 141 SER HXT H N N 142 # 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 GLN N CA sing N N 1 GLN N H sing N N 2 GLN N H2 sing N N 3 GLN CA C sing N N 4 GLN CA CB sing N N 5 GLN CA HA sing N N 6 GLN C O doub N N 7 GLN C OXT sing N N 8 GLN CB CG sing N N 9 GLN CB HB2 sing N N 10 GLN CB HB3 sing N N 11 GLN CG CD sing N N 12 GLN CG HG2 sing N N 13 GLN CG HG3 sing N N 14 GLN CD OE1 doub N N 15 GLN CD NE2 sing N N 16 GLN NE2 HE21 sing N N 17 GLN NE2 HE22 sing N N 18 GLN OXT HXT sing N N 19 HIS N CA sing N N 20 HIS N H sing N N 21 HIS N H2 sing N N 22 HIS CA C sing N N 23 HIS CA CB sing N N 24 HIS CA HA sing N N 25 HIS C O doub N N 26 HIS C OXT sing N N 27 HIS CB CG sing N N 28 HIS CB HB2 sing N N 29 HIS CB HB3 sing N N 30 HIS CG ND1 sing Y N 31 HIS CG CD2 doub Y N 32 HIS ND1 CE1 doub Y N 33 HIS ND1 HD1 sing N N 34 HIS CD2 NE2 sing Y N 35 HIS CD2 HD2 sing N N 36 HIS CE1 NE2 sing Y N 37 HIS CE1 HE1 sing N N 38 HIS NE2 HE2 sing N N 39 HIS OXT HXT sing N N 40 ILE N CA sing N N 41 ILE N H sing N N 42 ILE N H2 sing N N 43 ILE CA C sing N N 44 ILE CA CB sing N N 45 ILE CA HA sing N N 46 ILE C O doub N N 47 ILE C OXT sing N N 48 ILE CB CG1 sing N N 49 ILE CB CG2 sing N N 50 ILE CB HB sing N N 51 ILE CG1 CD1 sing N N 52 ILE CG1 HG12 sing N N 53 ILE CG1 HG13 sing N N 54 ILE CG2 HG21 sing N N 55 ILE CG2 HG22 sing N N 56 ILE CG2 HG23 sing N N 57 ILE CD1 HD11 sing N N 58 ILE CD1 HD12 sing N N 59 ILE CD1 HD13 sing N N 60 ILE OXT HXT sing N N 61 LEU N CA sing N N 62 LEU N H sing N N 63 LEU N H2 sing N N 64 LEU CA C sing N N 65 LEU CA CB sing N N 66 LEU CA HA sing N N 67 LEU C O doub N N 68 LEU C OXT sing N N 69 LEU CB CG sing N N 70 LEU CB HB2 sing N N 71 LEU CB HB3 sing N N 72 LEU CG CD1 sing N N 73 LEU CG CD2 sing N N 74 LEU CG HG sing N N 75 LEU CD1 HD11 sing N N 76 LEU CD1 HD12 sing N N 77 LEU CD1 HD13 sing N N 78 LEU CD2 HD21 sing N N 79 LEU CD2 HD22 sing N N 80 LEU CD2 HD23 sing N N 81 LEU OXT HXT sing N N 82 MET N CA sing N N 83 MET N H sing N N 84 MET N H2 sing N N 85 MET CA C sing N N 86 MET CA CB sing N N 87 MET CA HA sing N N 88 MET C O doub N N 89 MET C OXT sing N N 90 MET CB CG sing N N 91 MET CB HB2 sing N N 92 MET CB HB3 sing N N 93 MET CG SD sing N N 94 MET CG HG2 sing N N 95 MET CG HG3 sing N N 96 MET SD CE sing N N 97 MET CE HE1 sing N N 98 MET CE HE2 sing N N 99 MET CE HE3 sing N N 100 MET OXT HXT sing N N 101 PHE N CA sing N N 102 PHE N H sing N N 103 PHE N H2 sing N N 104 PHE CA C sing N N 105 PHE CA CB sing N N 106 PHE CA HA sing N N 107 PHE C O doub N N 108 PHE C OXT sing N N 109 PHE CB CG sing N N 110 PHE CB HB2 sing N N 111 PHE CB HB3 sing N N 112 PHE CG CD1 doub Y N 113 PHE CG CD2 sing Y N 114 PHE CD1 CE1 sing Y N 115 PHE CD1 HD1 sing N N 116 PHE CD2 CE2 doub Y N 117 PHE CD2 HD2 sing N N 118 PHE CE1 CZ doub Y N 119 PHE CE1 HE1 sing N N 120 PHE CE2 CZ sing Y N 121 PHE CE2 HE2 sing N N 122 PHE CZ HZ sing N N 123 PHE OXT HXT sing N N 124 SER N CA sing N N 125 SER N H sing N N 126 SER N H2 sing N N 127 SER CA C sing N N 128 SER CA CB sing N N 129 SER CA HA sing N N 130 SER C O doub N N 131 SER C OXT sing N N 132 SER CB OG sing N N 133 SER CB HB2 sing N N 134 SER CB HB3 sing N N 135 SER OG HG sing N N 136 SER OXT HXT sing N N 137 # _em_admin.current_status REL _em_admin.deposition_date 2025-08-31 _em_admin.deposition_site RCSB _em_admin.entry_id 9Y1V _em_admin.last_update 2026-09-09 _em_admin.map_release_date 2026-09-09 _em_admin.title 'Cryo-EM structure of designed Orb2 amyloid (FIMMF, polymorph 2)' # loop_ _em_buffer_component.buffer_id _em_buffer_component.concentration _em_buffer_component.concentration_units _em_buffer_component.formula _em_buffer_component.id _em_buffer_component.name 1 10 mM C8H18N2O4S 1 HEPES 1 75 mM NaCl 2 'Sodium Chloride' 1 20 mg/ml C3H8O3 3 Glycerol 1 2 mM MgCl2 4 'Magnesium Chloride' 1 10 mM KCl 5 'Potassium Chloride' # _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_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.experimental_flag YES _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units KILODALTONS/NANOMETER _em_entity_assembly_molwt.value 4 # _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 7227 _em_entity_assembly_naturalsource.organism 'Drosophila melanogaster' _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_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time 6.25 _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 60 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'TFS FALCON 4i (4k 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 1 _em_image_recording.num_real_images 5994 # _em_imaging_optics.chr_aberration_corrector ? _em_imaging_optics.energyfilter_lower ? _em_imaging_optics.energyfilter_slit_width 10 _em_imaging_optics.energyfilter_name 'TFS Selectris' _em_imaging_optics.energyfilter_upper ? _em_imaging_optics.id 1 _em_imaging_optics.imaging_id 1 _em_imaging_optics.phase_plate ? _em_imaging_optics.sph_aberration_corrector ? _em_imaging_optics.details ? # _em_particle_selection.details ? _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.method ? _em_particle_selection.num_particles_selected 2192140 _em_particle_selection.reference_model ? # 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' GUI 1 1 ? ? RELION 5.0-Beta-1 ? 'IMAGE ACQUISITION' ? 2 ? ? 1 SerialEM 4.0 ? MASKING ? 3 ? ? ? ? ? ? 'CTF CORRECTION' GUI 4 1 ? ? CTFFIND ? ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? Coot 0.9.8.96 ? OTHER ? 8 ? ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 9 1 ? ? RELION 5.0-beta-1-commit-b75b38 ? 'FINAL EULER ASSIGNMENT' ? 10 1 ? ? RELION 5.0-beta-1-commit-b75b38 ? CLASSIFICATION ? 11 1 ? ? RELION 5.0-beta-1-commit-b75b38 ? RECONSTRUCTION ? 12 1 ? ? RELION 5.0-beta-1-commit-b75b38 ? 'MODEL REFINEMENT' ? 13 ? 1 ? PHENIX 1.21 ? # _em_specimen.concentration 0.5 _em_specimen.details Homogenous _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Chan Zuckerberg Initiative' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number CP2-1-0000000296 _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 9Y1V _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 H N O S # loop_ #