data_8OKR # _entry.id 8OKR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _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 8OKR pdb_00008okr 10.2210/pdb8okr/pdb WWPDB D_1292129166 ? ? EMDB EMD-16930 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'virus enhancing amyloid fibril formed by CKFKFQF' _pdbx_database_related.db_id EMD-16930 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8OKR _pdbx_database_status.recvd_initial_deposition_date 2023-03-29 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Heerde, T.' 1 0000-0002-2142-3120 'Schmidt, M.' 2 0000-0002-9442-460X 'Faendrich, M.' 3 0000-0003-2123-6816 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 14 _citation.language ? _citation.page_first 4293 _citation.page_last 4293 _citation.title 'Cryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-023-40042-1 _citation.pdbx_database_id_PubMed 37464004 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Heerde, T.' 1 0000-0002-2142-3120 primary 'Schutz, D.' 2 ? primary 'Lin, Y.J.' 3 ? primary 'Munch, J.' 4 0000-0001-7316-7141 primary 'Schmidt, M.' 5 0000-0002-9442-460X primary 'Fandrich, M.' 6 0000-0003-2123-6816 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description PNF-18 _entity.formula_weight 949.168 _entity.pdbx_number_of_molecules 24 _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 CKFKFQF _entity_poly.pdbx_seq_one_letter_code_can CKFKFQF _entity_poly.pdbx_strand_id S,T,U,V,W,X,M,N,O,P,Q,R,G,H,I,J,K,L,A,B,C,D,E,F _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 CYS n 1 2 LYS n 1 3 PHE n 1 4 LYS n 1 5 PHE n 1 6 GLN n 1 7 PHE 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 7 _pdbx_entity_src_syn.organism_scientific 'HIV whole-genome vector AA1305#18' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 672471 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8OKR _struct_ref.pdbx_db_accession 8OKR _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 8OKR S 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 2 1 8OKR T 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 3 1 8OKR U 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 4 1 8OKR V 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 5 1 8OKR W 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 6 1 8OKR X 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 7 1 8OKR M 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 8 1 8OKR N 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 9 1 8OKR O 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 10 1 8OKR P 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 11 1 8OKR Q 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 12 1 8OKR R 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 13 1 8OKR G 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 14 1 8OKR H 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 15 1 8OKR I 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 16 1 8OKR J 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 17 1 8OKR K 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 18 1 8OKR L 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 19 1 8OKR A 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 20 1 8OKR B 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 21 1 8OKR C 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 22 1 8OKR D 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 23 1 8OKR E 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 24 1 8OKR F 1 ? 7 ? 8OKR 1 ? 7 ? 1 7 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 # _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 8OKR _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 8OKR _struct.title 'virus enhancing amyloid fibril formed by CKFKFQF' _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 8OKR _struct_keywords.text 'virus enhancing amyloid fibril, protein fibril, prion' _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 ? E N N 1 ? F N N 1 ? G N N 1 ? H N N 1 ? I N N 1 ? J N N 1 ? K N N 1 ? L N N 1 ? M N N 1 ? N N N 1 ? O N N 1 ? P N N 1 ? Q N N 1 ? R N N 1 ? S N N 1 ? T N N 1 ? U N N 1 ? V N N 1 ? W N N 1 ? X N N 1 ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 4 ? AA3 ? 4 ? AA4 ? 4 ? AA5 ? 4 ? AA6 ? 4 ? # 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 AA1 3 4 ? parallel AA2 1 2 ? parallel AA2 2 3 ? parallel AA2 3 4 ? parallel AA3 1 2 ? parallel AA3 2 3 ? parallel AA3 3 4 ? parallel AA4 1 2 ? parallel AA4 2 3 ? parallel AA4 3 4 ? parallel AA5 1 2 ? parallel AA5 2 3 ? parallel AA5 3 4 ? parallel AA6 1 2 ? parallel AA6 2 3 ? parallel AA6 3 4 ? 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 PHE A 3 ? GLN A 6 ? PHE S 3 GLN S 6 AA1 2 PHE G 3 ? GLN G 6 ? PHE M 3 GLN M 6 AA1 3 PHE M 3 ? GLN M 6 ? PHE G 3 GLN G 6 AA1 4 PHE S 3 ? GLN S 6 ? PHE A 3 GLN A 6 AA2 1 PHE B 3 ? GLN B 6 ? PHE T 3 GLN T 6 AA2 2 PHE H 3 ? GLN H 6 ? PHE N 3 GLN N 6 AA2 3 PHE N 3 ? GLN N 6 ? PHE H 3 GLN H 6 AA2 4 PHE T 3 ? GLN T 6 ? PHE B 3 GLN B 6 AA3 1 PHE C 3 ? GLN C 6 ? PHE U 3 GLN U 6 AA3 2 PHE I 3 ? GLN I 6 ? PHE O 3 GLN O 6 AA3 3 PHE O 3 ? GLN O 6 ? PHE I 3 GLN I 6 AA3 4 PHE U 3 ? GLN U 6 ? PHE C 3 GLN C 6 AA4 1 PHE D 3 ? GLN D 6 ? PHE V 3 GLN V 6 AA4 2 PHE J 3 ? GLN J 6 ? PHE P 3 GLN P 6 AA4 3 PHE P 3 ? GLN P 6 ? PHE J 3 GLN J 6 AA4 4 PHE V 3 ? GLN V 6 ? PHE D 3 GLN D 6 AA5 1 PHE E 3 ? GLN E 6 ? PHE W 3 GLN W 6 AA5 2 PHE K 3 ? GLN K 6 ? PHE Q 3 GLN Q 6 AA5 3 PHE Q 3 ? GLN Q 6 ? PHE K 3 GLN K 6 AA5 4 PHE W 3 ? GLN W 6 ? PHE E 3 GLN E 6 AA6 1 PHE F 3 ? GLN F 6 ? PHE X 3 GLN X 6 AA6 2 PHE L 3 ? GLN L 6 ? PHE R 3 GLN R 6 AA6 3 PHE R 3 ? GLN R 6 ? PHE L 3 GLN L 6 AA6 4 PHE X 3 ? GLN X 6 ? PHE F 3 GLN F 6 # 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 GLN A 6 ? N GLN S 6 O PHE G 5 ? O PHE M 5 AA1 2 3 N GLN G 6 ? N GLN M 6 O PHE M 5 ? O PHE G 5 AA1 3 4 N GLN M 6 ? N GLN G 6 O PHE S 5 ? O PHE A 5 AA2 1 2 N LYS B 4 ? N LYS T 4 O PHE H 5 ? O PHE N 5 AA2 2 3 N LYS H 4 ? N LYS N 4 O PHE N 5 ? O PHE H 5 AA2 3 4 N LYS N 4 ? N LYS H 4 O PHE T 5 ? O PHE B 5 AA3 1 2 N LYS C 4 ? N LYS U 4 O PHE I 5 ? O PHE O 5 AA3 2 3 N LYS I 4 ? N LYS O 4 O PHE O 5 ? O PHE I 5 AA3 3 4 N LYS O 4 ? N LYS I 4 O PHE U 5 ? O PHE C 5 AA4 1 2 N GLN D 6 ? N GLN V 6 O PHE J 5 ? O PHE P 5 AA4 2 3 N GLN J 6 ? N GLN P 6 O PHE P 5 ? O PHE J 5 AA4 3 4 N GLN P 6 ? N GLN J 6 O PHE V 5 ? O PHE D 5 AA5 1 2 N LYS E 4 ? N LYS W 4 O PHE K 5 ? O PHE Q 5 AA5 2 3 N LYS K 4 ? N LYS Q 4 O PHE Q 5 ? O PHE K 5 AA5 3 4 N LYS Q 4 ? N LYS K 4 O PHE W 5 ? O PHE E 5 AA6 1 2 N LYS F 4 ? N LYS X 4 O PHE L 5 ? O PHE R 5 AA6 2 3 N LYS L 4 ? N LYS R 4 O PHE R 5 ? O PHE L 5 AA6 3 4 N LYS R 4 ? N LYS L 4 O PHE X 5 ? O PHE F 5 # _atom_sites.entry_id 8OKR _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 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 S # 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 CYS 1 1 1 CYS CYS S . n A 1 2 LYS 2 2 2 LYS LYS S . n A 1 3 PHE 3 3 3 PHE PHE S . n A 1 4 LYS 4 4 4 LYS LYS S . n A 1 5 PHE 5 5 5 PHE PHE S . n A 1 6 GLN 6 6 6 GLN GLN S . n A 1 7 PHE 7 7 7 PHE PHE S . n B 1 1 CYS 1 1 1 CYS CYS T . n B 1 2 LYS 2 2 2 LYS LYS T . n B 1 3 PHE 3 3 3 PHE PHE T . n B 1 4 LYS 4 4 4 LYS LYS T . n B 1 5 PHE 5 5 5 PHE PHE T . n B 1 6 GLN 6 6 6 GLN GLN T . n B 1 7 PHE 7 7 7 PHE PHE T . n C 1 1 CYS 1 1 1 CYS CYS U . n C 1 2 LYS 2 2 2 LYS LYS U . n C 1 3 PHE 3 3 3 PHE PHE U . n C 1 4 LYS 4 4 4 LYS LYS U . n C 1 5 PHE 5 5 5 PHE PHE U . n C 1 6 GLN 6 6 6 GLN GLN U . n C 1 7 PHE 7 7 7 PHE PHE U . n D 1 1 CYS 1 1 1 CYS CYS V . n D 1 2 LYS 2 2 2 LYS LYS V . n D 1 3 PHE 3 3 3 PHE PHE V . n D 1 4 LYS 4 4 4 LYS LYS V . n D 1 5 PHE 5 5 5 PHE PHE V . n D 1 6 GLN 6 6 6 GLN GLN V . n D 1 7 PHE 7 7 7 PHE PHE V . n E 1 1 CYS 1 1 1 CYS CYS W . n E 1 2 LYS 2 2 2 LYS LYS W . n E 1 3 PHE 3 3 3 PHE PHE W . n E 1 4 LYS 4 4 4 LYS LYS W . n E 1 5 PHE 5 5 5 PHE PHE W . n E 1 6 GLN 6 6 6 GLN GLN W . n E 1 7 PHE 7 7 7 PHE PHE W . n F 1 1 CYS 1 1 1 CYS CYS X . n F 1 2 LYS 2 2 2 LYS LYS X . n F 1 3 PHE 3 3 3 PHE PHE X . n F 1 4 LYS 4 4 4 LYS LYS X . n F 1 5 PHE 5 5 5 PHE PHE X . n F 1 6 GLN 6 6 6 GLN GLN X . n F 1 7 PHE 7 7 7 PHE PHE X . n G 1 1 CYS 1 1 1 CYS CYS M . n G 1 2 LYS 2 2 2 LYS LYS M . n G 1 3 PHE 3 3 3 PHE PHE M . n G 1 4 LYS 4 4 4 LYS LYS M . n G 1 5 PHE 5 5 5 PHE PHE M . n G 1 6 GLN 6 6 6 GLN GLN M . n G 1 7 PHE 7 7 7 PHE PHE M . n H 1 1 CYS 1 1 1 CYS CYS N . n H 1 2 LYS 2 2 2 LYS LYS N . n H 1 3 PHE 3 3 3 PHE PHE N . n H 1 4 LYS 4 4 4 LYS LYS N . n H 1 5 PHE 5 5 5 PHE PHE N . n H 1 6 GLN 6 6 6 GLN GLN N . n H 1 7 PHE 7 7 7 PHE PHE N . n I 1 1 CYS 1 1 1 CYS CYS O . n I 1 2 LYS 2 2 2 LYS LYS O . n I 1 3 PHE 3 3 3 PHE PHE O . n I 1 4 LYS 4 4 4 LYS LYS O . n I 1 5 PHE 5 5 5 PHE PHE O . n I 1 6 GLN 6 6 6 GLN GLN O . n I 1 7 PHE 7 7 7 PHE PHE O . n J 1 1 CYS 1 1 1 CYS CYS P . n J 1 2 LYS 2 2 2 LYS LYS P . n J 1 3 PHE 3 3 3 PHE PHE P . n J 1 4 LYS 4 4 4 LYS LYS P . n J 1 5 PHE 5 5 5 PHE PHE P . n J 1 6 GLN 6 6 6 GLN GLN P . n J 1 7 PHE 7 7 7 PHE PHE P . n K 1 1 CYS 1 1 1 CYS CYS Q . n K 1 2 LYS 2 2 2 LYS LYS Q . n K 1 3 PHE 3 3 3 PHE PHE Q . n K 1 4 LYS 4 4 4 LYS LYS Q . n K 1 5 PHE 5 5 5 PHE PHE Q . n K 1 6 GLN 6 6 6 GLN GLN Q . n K 1 7 PHE 7 7 7 PHE PHE Q . n L 1 1 CYS 1 1 1 CYS CYS R . n L 1 2 LYS 2 2 2 LYS LYS R . n L 1 3 PHE 3 3 3 PHE PHE R . n L 1 4 LYS 4 4 4 LYS LYS R . n L 1 5 PHE 5 5 5 PHE PHE R . n L 1 6 GLN 6 6 6 GLN GLN R . n L 1 7 PHE 7 7 7 PHE PHE R . n M 1 1 CYS 1 1 1 CYS CYS G . n M 1 2 LYS 2 2 2 LYS LYS G . n M 1 3 PHE 3 3 3 PHE PHE G . n M 1 4 LYS 4 4 4 LYS LYS G . n M 1 5 PHE 5 5 5 PHE PHE G . n M 1 6 GLN 6 6 6 GLN GLN G . n M 1 7 PHE 7 7 7 PHE PHE G . n N 1 1 CYS 1 1 1 CYS CYS H . n N 1 2 LYS 2 2 2 LYS LYS H . n N 1 3 PHE 3 3 3 PHE PHE H . n N 1 4 LYS 4 4 4 LYS LYS H . n N 1 5 PHE 5 5 5 PHE PHE H . n N 1 6 GLN 6 6 6 GLN GLN H . n N 1 7 PHE 7 7 7 PHE PHE H . n O 1 1 CYS 1 1 1 CYS CYS I . n O 1 2 LYS 2 2 2 LYS LYS I . n O 1 3 PHE 3 3 3 PHE PHE I . n O 1 4 LYS 4 4 4 LYS LYS I . n O 1 5 PHE 5 5 5 PHE PHE I . n O 1 6 GLN 6 6 6 GLN GLN I . n O 1 7 PHE 7 7 7 PHE PHE I . n P 1 1 CYS 1 1 1 CYS CYS J . n P 1 2 LYS 2 2 2 LYS LYS J . n P 1 3 PHE 3 3 3 PHE PHE J . n P 1 4 LYS 4 4 4 LYS LYS J . n P 1 5 PHE 5 5 5 PHE PHE J . n P 1 6 GLN 6 6 6 GLN GLN J . n P 1 7 PHE 7 7 7 PHE PHE J . n Q 1 1 CYS 1 1 1 CYS CYS K . n Q 1 2 LYS 2 2 2 LYS LYS K . n Q 1 3 PHE 3 3 3 PHE PHE K . n Q 1 4 LYS 4 4 4 LYS LYS K . n Q 1 5 PHE 5 5 5 PHE PHE K . n Q 1 6 GLN 6 6 6 GLN GLN K . n Q 1 7 PHE 7 7 7 PHE PHE K . n R 1 1 CYS 1 1 1 CYS CYS L . n R 1 2 LYS 2 2 2 LYS LYS L . n R 1 3 PHE 3 3 3 PHE PHE L . n R 1 4 LYS 4 4 4 LYS LYS L . n R 1 5 PHE 5 5 5 PHE PHE L . n R 1 6 GLN 6 6 6 GLN GLN L . n R 1 7 PHE 7 7 7 PHE PHE L . n S 1 1 CYS 1 1 1 CYS CYS A . n S 1 2 LYS 2 2 2 LYS LYS A . n S 1 3 PHE 3 3 3 PHE PHE A . n S 1 4 LYS 4 4 4 LYS LYS A . n S 1 5 PHE 5 5 5 PHE PHE A . n S 1 6 GLN 6 6 6 GLN GLN A . n S 1 7 PHE 7 7 7 PHE PHE A . n T 1 1 CYS 1 1 1 CYS CYS B . n T 1 2 LYS 2 2 2 LYS LYS B . n T 1 3 PHE 3 3 3 PHE PHE B . n T 1 4 LYS 4 4 4 LYS LYS B . n T 1 5 PHE 5 5 5 PHE PHE B . n T 1 6 GLN 6 6 6 GLN GLN B . n T 1 7 PHE 7 7 7 PHE PHE B . n U 1 1 CYS 1 1 1 CYS CYS C . n U 1 2 LYS 2 2 2 LYS LYS C . n U 1 3 PHE 3 3 3 PHE PHE C . n U 1 4 LYS 4 4 4 LYS LYS C . n U 1 5 PHE 5 5 5 PHE PHE C . n U 1 6 GLN 6 6 6 GLN GLN C . n U 1 7 PHE 7 7 7 PHE PHE C . n V 1 1 CYS 1 1 1 CYS CYS D . n V 1 2 LYS 2 2 2 LYS LYS D . n V 1 3 PHE 3 3 3 PHE PHE D . n V 1 4 LYS 4 4 4 LYS LYS D . n V 1 5 PHE 5 5 5 PHE PHE D . n V 1 6 GLN 6 6 6 GLN GLN D . n V 1 7 PHE 7 7 7 PHE PHE D . n W 1 1 CYS 1 1 1 CYS CYS E . n W 1 2 LYS 2 2 2 LYS LYS E . n W 1 3 PHE 3 3 3 PHE PHE E . n W 1 4 LYS 4 4 4 LYS LYS E . n W 1 5 PHE 5 5 5 PHE PHE E . n W 1 6 GLN 6 6 6 GLN GLN E . n W 1 7 PHE 7 7 7 PHE PHE E . n X 1 1 CYS 1 1 1 CYS CYS F . n X 1 2 LYS 2 2 2 LYS LYS F . n X 1 3 PHE 3 3 3 PHE PHE F . n X 1 4 LYS 4 4 4 LYS LYS F . n X 1 5 PHE 5 5 5 PHE PHE F . n X 1 6 GLN 6 6 6 GLN GLN F . n X 1 7 PHE 7 7 7 PHE PHE F . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email marcus.faendrich@uni-ulm.de _pdbx_contact_author.name_first Marcus _pdbx_contact_author.name_last Faendrich _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-2123-6816 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 # _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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 20610 ? 1 MORE -113 ? 1 'SSA (A^2)' 8470 ? # _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 ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2023-08-02 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 8OKR _em_3d_fitting.method ? _em_3d_fitting.target_criteria 'correlation coefficient' _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space REAL _em_3d_fitting.ref_protocol 'BACKBONE TRACE' # _em_3d_reconstruction.entry_id 8OKR _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 2.86 _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 25550 _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 '50 mM 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid' _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 'virus enhancing amyloid' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_image_scans.entry_id 8OKR _em_image_scans.id 1 _em_image_scans.number_digital_images ? _em_image_scans.details ? _em_image_scans.scanner_model ? _em_image_scans.sampling_size ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.citation_id ? _em_image_scans.dimension_height ? _em_image_scans.dimension_width ? _em_image_scans.frames_per_image 40 _em_image_scans.image_recording_id 1 _em_image_scans.used_frames_per_image ? # _em_imaging.entry_id 8OKR _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TITAN 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 2.70 _em_imaging.nominal_defocus_min 800 _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 NITROGEN # _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 400 _em_sample_support.grid_type C-flat-1.2/1.3 _em_sample_support.details ? _em_sample_support.specimen_id 1 _em_sample_support.citation_id ? # _em_vitrification.entry_id 8OKR _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 96 _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument 'FEI VITROBOT MARK III' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 8OKR _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _em_experiment.aggregation_state 'HELICAL ARRAY' _em_experiment.entity_assembly_id 1 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 NZ Q LYS 4 ? ? O J PHE 7 ? ? 1.49 2 1 NZ N LYS 4 ? ? O G PHE 7 ? ? 1.49 3 1 NZ T LYS 4 ? ? O M PHE 7 ? ? 1.49 4 1 NZ W LYS 4 ? ? O P PHE 7 ? ? 1.49 5 1 NZ H LYS 4 ? ? O A PHE 7 ? ? 1.49 6 1 NZ K LYS 4 ? ? O D PHE 7 ? ? 1.49 # _em_buffer_component.buffer_id 1 _em_buffer_component.concentration 50 _em_buffer_component.concentration_units mM _em_buffer_component.formula C8H18N2O4S _em_buffer_component.id 1 _em_buffer_component.name '2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid' # _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 NO _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _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_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 562 _em_entity_assembly_recombinant.organism 'Escherichia coli' _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 -2.61 _em_helical_entity.axial_rise_per_subunit 4.8 # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time 8 _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 45 _em_image_recording.details ? _em_image_recording.detector_mode COUNTING _em_image_recording.film_or_detector_model 'GATAN K2 SUMMIT (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 ? _em_image_recording.num_real_images ? # _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 356134 _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 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 SerialEM ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? Gctf ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? Coot 0.8.9 OTHER ? 8 ? ? ? ? ? 'MODEL REFINEMENT' ? 9 ? 1 ? PHENIX 1.16-3549 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? RELION 3.0.4 RECONSTRUCTION ? 13 1 ? ? RELION 3.1 # _em_specimen.concentration 0.3 _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 # _pdbx_audit_support.funding_organization 'German Research Foundation (DFG)' _pdbx_audit_support.country Germany _pdbx_audit_support.grant_number 'CRC 1279/2 project A03' _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details ? #