data_7QV6 # _entry.id 7QV6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 7QV6 pdb_00007qv6 10.2210/pdb7qv6/pdb WWPDB D_1292120105 ? ? EMDB EMD-14168 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2022-06-29 2 'Structure model' 1 1 2022-08-10 3 'Structure model' 1 2 2024-07-17 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' em_admin # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.journal_volume' 6 2 'Structure model' '_citation.page_first' 7 2 'Structure model' '_citation.page_last' 8 2 'Structure model' '_citation.pdbx_database_id_DOI' 9 2 'Structure model' '_citation.pdbx_database_id_PubMed' 10 2 'Structure model' '_citation.title' 11 2 'Structure model' '_citation.year' 12 2 'Structure model' '_citation_author.identifier_ORCID' 13 2 'Structure model' '_citation_author.name' 14 3 'Structure model' '_em_admin.last_update' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7QV6 _pdbx_database_status.recvd_initial_deposition_date 2022-01-19 _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 # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Amyloid fibril from the antimicrobial peptide aurein 3.3' _pdbx_database_related.db_id EMD-14168 _pdbx_database_related.content_type 'associated EM volume' # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 2 mlandau@technion.ac.il Meytal Landau ? 'principal investigator/group leader' 0000-0002-1743-3430 3 kay.gruenewald@cssb-hamburg.de Kay Gruenewald ? 'principal investigator/group leader' 0000-0002-4788-2691 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Buecker, R.' 1 0000-0001-7654-4707 'Seuring, C.' 2 0000-0003-1000-0859 'Cazey, C.' 3 ? 'Veith, K.' 4 0000-0001-7454-5490 'Garcia-Alai, M.' 5 0000-0002-5200-7816 'Gruenewald, K.' 6 0000-0002-4788-2691 'Landau, M.' 7 0000-0002-1743-3430 # _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 13 _citation.language ? _citation.page_first 4356 _citation.page_last 4356 _citation.title 'The Cryo-EM structures of two amphibian antimicrobial cross-beta amyloid fibrils.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-022-32039-z _citation.pdbx_database_id_PubMed 35896552 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bucker, R.' 1 ? primary 'Seuring, C.' 2 0000-0003-1000-0859 primary 'Cazey, C.' 3 ? primary 'Veith, K.' 4 ? primary 'Garcia-Alai, M.' 5 0000-0002-5200-7816 primary 'Grunewald, K.' 6 0000-0002-4788-2691 primary 'Landau, M.' 7 0000-0002-1743-3430 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description Aurein-3.3 _entity.formula_weight 1800.171 _entity.pdbx_number_of_molecules 18 _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 GLFDIVKKIAGHIVSSI _entity_poly.pdbx_seq_one_letter_code_can GLFDIVKKIAGHIVSSI _entity_poly.pdbx_strand_id B,A,E,D,C,F,H,G,K,J,I,L,N,M,Q,P,O,R _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 LEU n 1 3 PHE n 1 4 ASP n 1 5 ILE n 1 6 VAL n 1 7 LYS n 1 8 LYS n 1 9 ILE n 1 10 ALA n 1 11 GLY n 1 12 HIS n 1 13 ILE n 1 14 VAL n 1 15 SER n 1 16 SER n 1 17 ILE 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 17 _pdbx_entity_src_syn.organism_scientific 'Ranoidea raniformis' _pdbx_entity_src_syn.organism_common_name 'blue-thighed treefrog' _pdbx_entity_src_syn.ncbi_taxonomy_id 116057 _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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 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 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 1 1 GLY GLY B . n A 1 2 LEU 2 2 2 LEU LEU B . n A 1 3 PHE 3 3 3 PHE PHE B . n A 1 4 ASP 4 4 4 ASP ASP B . n A 1 5 ILE 5 5 5 ILE ILE B . n A 1 6 VAL 6 6 6 VAL VAL B . n A 1 7 LYS 7 7 7 LYS LYS B . n A 1 8 LYS 8 8 8 LYS LYS B . n A 1 9 ILE 9 9 9 ILE ILE B . n A 1 10 ALA 10 10 10 ALA ALA B . n A 1 11 GLY 11 11 11 GLY GLY B . n A 1 12 HIS 12 12 12 HIS HIS B . n A 1 13 ILE 13 13 13 ILE ILE B . n A 1 14 VAL 14 14 14 VAL VAL B . n A 1 15 SER 15 15 15 SER SER B . n A 1 16 SER 16 16 16 SER SER B . n A 1 17 ILE 17 17 17 ILE ILE B . n B 1 1 GLY 1 1 1 GLY GLY A . n B 1 2 LEU 2 2 2 LEU LEU A . n B 1 3 PHE 3 3 3 PHE PHE A . n B 1 4 ASP 4 4 4 ASP ASP A . n B 1 5 ILE 5 5 5 ILE ILE A . n B 1 6 VAL 6 6 6 VAL VAL A . n B 1 7 LYS 7 7 7 LYS LYS A . n B 1 8 LYS 8 8 8 LYS LYS A . n B 1 9 ILE 9 9 9 ILE ILE A . n B 1 10 ALA 10 10 10 ALA ALA A . n B 1 11 GLY 11 11 11 GLY GLY A . n B 1 12 HIS 12 12 12 HIS HIS A . n B 1 13 ILE 13 13 13 ILE ILE A . n B 1 14 VAL 14 14 14 VAL VAL A . n B 1 15 SER 15 15 15 SER SER A . n B 1 16 SER 16 16 16 SER SER A . n B 1 17 ILE 17 17 17 ILE ILE A . n C 1 1 GLY 1 1 1 GLY GLY E . n C 1 2 LEU 2 2 2 LEU LEU E . n C 1 3 PHE 3 3 3 PHE PHE E . n C 1 4 ASP 4 4 4 ASP ASP E . n C 1 5 ILE 5 5 5 ILE ILE E . n C 1 6 VAL 6 6 6 VAL VAL E . n C 1 7 LYS 7 7 7 LYS LYS E . n C 1 8 LYS 8 8 8 LYS LYS E . n C 1 9 ILE 9 9 9 ILE ILE E . n C 1 10 ALA 10 10 10 ALA ALA E . n C 1 11 GLY 11 11 11 GLY GLY E . n C 1 12 HIS 12 12 12 HIS HIS E . n C 1 13 ILE 13 13 13 ILE ILE E . n C 1 14 VAL 14 14 14 VAL VAL E . n C 1 15 SER 15 15 15 SER SER E . n C 1 16 SER 16 16 16 SER SER E . n C 1 17 ILE 17 17 17 ILE ILE E . n D 1 1 GLY 1 1 1 GLY GLY D . n D 1 2 LEU 2 2 2 LEU LEU D . n D 1 3 PHE 3 3 3 PHE PHE D . n D 1 4 ASP 4 4 4 ASP ASP D . n D 1 5 ILE 5 5 5 ILE ILE D . n D 1 6 VAL 6 6 6 VAL VAL D . n D 1 7 LYS 7 7 7 LYS LYS D . n D 1 8 LYS 8 8 8 LYS LYS D . n D 1 9 ILE 9 9 9 ILE ILE D . n D 1 10 ALA 10 10 10 ALA ALA D . n D 1 11 GLY 11 11 11 GLY GLY D . n D 1 12 HIS 12 12 12 HIS HIS D . n D 1 13 ILE 13 13 13 ILE ILE D . n D 1 14 VAL 14 14 14 VAL VAL D . n D 1 15 SER 15 15 15 SER SER D . n D 1 16 SER 16 16 16 SER SER D . n D 1 17 ILE 17 17 17 ILE ILE D . n E 1 1 GLY 1 1 1 GLY GLY C . n E 1 2 LEU 2 2 2 LEU LEU C . n E 1 3 PHE 3 3 3 PHE PHE C . n E 1 4 ASP 4 4 4 ASP ASP C . n E 1 5 ILE 5 5 5 ILE ILE C . n E 1 6 VAL 6 6 6 VAL VAL C . n E 1 7 LYS 7 7 7 LYS LYS C . n E 1 8 LYS 8 8 8 LYS LYS C . n E 1 9 ILE 9 9 9 ILE ILE C . n E 1 10 ALA 10 10 10 ALA ALA C . n E 1 11 GLY 11 11 11 GLY GLY C . n E 1 12 HIS 12 12 12 HIS HIS C . n E 1 13 ILE 13 13 13 ILE ILE C . n E 1 14 VAL 14 14 14 VAL VAL C . n E 1 15 SER 15 15 15 SER SER C . n E 1 16 SER 16 16 16 SER SER C . n E 1 17 ILE 17 17 17 ILE ILE C . n F 1 1 GLY 1 1 1 GLY GLY F . n F 1 2 LEU 2 2 2 LEU LEU F . n F 1 3 PHE 3 3 3 PHE PHE F . n F 1 4 ASP 4 4 4 ASP ASP F . n F 1 5 ILE 5 5 5 ILE ILE F . n F 1 6 VAL 6 6 6 VAL VAL F . n F 1 7 LYS 7 7 7 LYS LYS F . n F 1 8 LYS 8 8 8 LYS LYS F . n F 1 9 ILE 9 9 9 ILE ILE F . n F 1 10 ALA 10 10 10 ALA ALA F . n F 1 11 GLY 11 11 11 GLY GLY F . n F 1 12 HIS 12 12 12 HIS HIS F . n F 1 13 ILE 13 13 13 ILE ILE F . n F 1 14 VAL 14 14 14 VAL VAL F . n F 1 15 SER 15 15 15 SER SER F . n F 1 16 SER 16 16 16 SER SER F . n F 1 17 ILE 17 17 17 ILE ILE F . n G 1 1 GLY 1 1 1 GLY GLY H . n G 1 2 LEU 2 2 2 LEU LEU H . n G 1 3 PHE 3 3 3 PHE PHE H . n G 1 4 ASP 4 4 4 ASP ASP H . n G 1 5 ILE 5 5 5 ILE ILE H . n G 1 6 VAL 6 6 6 VAL VAL H . n G 1 7 LYS 7 7 7 LYS LYS H . n G 1 8 LYS 8 8 8 LYS LYS H . n G 1 9 ILE 9 9 9 ILE ILE H . n G 1 10 ALA 10 10 10 ALA ALA H . n G 1 11 GLY 11 11 11 GLY GLY H . n G 1 12 HIS 12 12 12 HIS HIS H . n G 1 13 ILE 13 13 13 ILE ILE H . n G 1 14 VAL 14 14 14 VAL VAL H . n G 1 15 SER 15 15 15 SER SER H . n G 1 16 SER 16 16 16 SER SER H . n G 1 17 ILE 17 17 17 ILE ILE H . n H 1 1 GLY 1 1 1 GLY GLY G . n H 1 2 LEU 2 2 2 LEU LEU G . n H 1 3 PHE 3 3 3 PHE PHE G . n H 1 4 ASP 4 4 4 ASP ASP G . n H 1 5 ILE 5 5 5 ILE ILE G . n H 1 6 VAL 6 6 6 VAL VAL G . n H 1 7 LYS 7 7 7 LYS LYS G . n H 1 8 LYS 8 8 8 LYS LYS G . n H 1 9 ILE 9 9 9 ILE ILE G . n H 1 10 ALA 10 10 10 ALA ALA G . n H 1 11 GLY 11 11 11 GLY GLY G . n H 1 12 HIS 12 12 12 HIS HIS G . n H 1 13 ILE 13 13 13 ILE ILE G . n H 1 14 VAL 14 14 14 VAL VAL G . n H 1 15 SER 15 15 15 SER SER G . n H 1 16 SER 16 16 16 SER SER G . n H 1 17 ILE 17 17 17 ILE ILE G . n I 1 1 GLY 1 1 1 GLY GLY K . n I 1 2 LEU 2 2 2 LEU LEU K . n I 1 3 PHE 3 3 3 PHE PHE K . n I 1 4 ASP 4 4 4 ASP ASP K . n I 1 5 ILE 5 5 5 ILE ILE K . n I 1 6 VAL 6 6 6 VAL VAL K . n I 1 7 LYS 7 7 7 LYS LYS K . n I 1 8 LYS 8 8 8 LYS LYS K . n I 1 9 ILE 9 9 9 ILE ILE K . n I 1 10 ALA 10 10 10 ALA ALA K . n I 1 11 GLY 11 11 11 GLY GLY K . n I 1 12 HIS 12 12 12 HIS HIS K . n I 1 13 ILE 13 13 13 ILE ILE K . n I 1 14 VAL 14 14 14 VAL VAL K . n I 1 15 SER 15 15 15 SER SER K . n I 1 16 SER 16 16 16 SER SER K . n I 1 17 ILE 17 17 17 ILE ILE K . n J 1 1 GLY 1 1 1 GLY GLY J . n J 1 2 LEU 2 2 2 LEU LEU J . n J 1 3 PHE 3 3 3 PHE PHE J . n J 1 4 ASP 4 4 4 ASP ASP J . n J 1 5 ILE 5 5 5 ILE ILE J . n J 1 6 VAL 6 6 6 VAL VAL J . n J 1 7 LYS 7 7 7 LYS LYS J . n J 1 8 LYS 8 8 8 LYS LYS J . n J 1 9 ILE 9 9 9 ILE ILE J . n J 1 10 ALA 10 10 10 ALA ALA J . n J 1 11 GLY 11 11 11 GLY GLY J . n J 1 12 HIS 12 12 12 HIS HIS J . n J 1 13 ILE 13 13 13 ILE ILE J . n J 1 14 VAL 14 14 14 VAL VAL J . n J 1 15 SER 15 15 15 SER SER J . n J 1 16 SER 16 16 16 SER SER J . n J 1 17 ILE 17 17 17 ILE ILE J . n K 1 1 GLY 1 1 1 GLY GLY I . n K 1 2 LEU 2 2 2 LEU LEU I . n K 1 3 PHE 3 3 3 PHE PHE I . n K 1 4 ASP 4 4 4 ASP ASP I . n K 1 5 ILE 5 5 5 ILE ILE I . n K 1 6 VAL 6 6 6 VAL VAL I . n K 1 7 LYS 7 7 7 LYS LYS I . n K 1 8 LYS 8 8 8 LYS LYS I . n K 1 9 ILE 9 9 9 ILE ILE I . n K 1 10 ALA 10 10 10 ALA ALA I . n K 1 11 GLY 11 11 11 GLY GLY I . n K 1 12 HIS 12 12 12 HIS HIS I . n K 1 13 ILE 13 13 13 ILE ILE I . n K 1 14 VAL 14 14 14 VAL VAL I . n K 1 15 SER 15 15 15 SER SER I . n K 1 16 SER 16 16 16 SER SER I . n K 1 17 ILE 17 17 17 ILE ILE I . n L 1 1 GLY 1 1 1 GLY GLY L . n L 1 2 LEU 2 2 2 LEU LEU L . n L 1 3 PHE 3 3 3 PHE PHE L . n L 1 4 ASP 4 4 4 ASP ASP L . n L 1 5 ILE 5 5 5 ILE ILE L . n L 1 6 VAL 6 6 6 VAL VAL L . n L 1 7 LYS 7 7 7 LYS LYS L . n L 1 8 LYS 8 8 8 LYS LYS L . n L 1 9 ILE 9 9 9 ILE ILE L . n L 1 10 ALA 10 10 10 ALA ALA L . n L 1 11 GLY 11 11 11 GLY GLY L . n L 1 12 HIS 12 12 12 HIS HIS L . n L 1 13 ILE 13 13 13 ILE ILE L . n L 1 14 VAL 14 14 14 VAL VAL L . n L 1 15 SER 15 15 15 SER SER L . n L 1 16 SER 16 16 16 SER SER L . n L 1 17 ILE 17 17 17 ILE ILE L . n M 1 1 GLY 1 1 1 GLY GLY N . n M 1 2 LEU 2 2 2 LEU LEU N . n M 1 3 PHE 3 3 3 PHE PHE N . n M 1 4 ASP 4 4 4 ASP ASP N . n M 1 5 ILE 5 5 5 ILE ILE N . n M 1 6 VAL 6 6 6 VAL VAL N . n M 1 7 LYS 7 7 7 LYS LYS N . n M 1 8 LYS 8 8 8 LYS LYS N . n M 1 9 ILE 9 9 9 ILE ILE N . n M 1 10 ALA 10 10 10 ALA ALA N . n M 1 11 GLY 11 11 11 GLY GLY N . n M 1 12 HIS 12 12 12 HIS HIS N . n M 1 13 ILE 13 13 13 ILE ILE N . n M 1 14 VAL 14 14 14 VAL VAL N . n M 1 15 SER 15 15 15 SER SER N . n M 1 16 SER 16 16 16 SER SER N . n M 1 17 ILE 17 17 17 ILE ILE N . n N 1 1 GLY 1 1 1 GLY GLY M . n N 1 2 LEU 2 2 2 LEU LEU M . n N 1 3 PHE 3 3 3 PHE PHE M . n N 1 4 ASP 4 4 4 ASP ASP M . n N 1 5 ILE 5 5 5 ILE ILE M . n N 1 6 VAL 6 6 6 VAL VAL M . n N 1 7 LYS 7 7 7 LYS LYS M . n N 1 8 LYS 8 8 8 LYS LYS M . n N 1 9 ILE 9 9 9 ILE ILE M . n N 1 10 ALA 10 10 10 ALA ALA M . n N 1 11 GLY 11 11 11 GLY GLY M . n N 1 12 HIS 12 12 12 HIS HIS M . n N 1 13 ILE 13 13 13 ILE ILE M . n N 1 14 VAL 14 14 14 VAL VAL M . n N 1 15 SER 15 15 15 SER SER M . n N 1 16 SER 16 16 16 SER SER M . n N 1 17 ILE 17 17 17 ILE ILE M . n O 1 1 GLY 1 1 1 GLY GLY Q . n O 1 2 LEU 2 2 2 LEU LEU Q . n O 1 3 PHE 3 3 3 PHE PHE Q . n O 1 4 ASP 4 4 4 ASP ASP Q . n O 1 5 ILE 5 5 5 ILE ILE Q . n O 1 6 VAL 6 6 6 VAL VAL Q . n O 1 7 LYS 7 7 7 LYS LYS Q . n O 1 8 LYS 8 8 8 LYS LYS Q . n O 1 9 ILE 9 9 9 ILE ILE Q . n O 1 10 ALA 10 10 10 ALA ALA Q . n O 1 11 GLY 11 11 11 GLY GLY Q . n O 1 12 HIS 12 12 12 HIS HIS Q . n O 1 13 ILE 13 13 13 ILE ILE Q . n O 1 14 VAL 14 14 14 VAL VAL Q . n O 1 15 SER 15 15 15 SER SER Q . n O 1 16 SER 16 16 16 SER SER Q . n O 1 17 ILE 17 17 17 ILE ILE Q . n P 1 1 GLY 1 1 1 GLY GLY P . n P 1 2 LEU 2 2 2 LEU LEU P . n P 1 3 PHE 3 3 3 PHE PHE P . n P 1 4 ASP 4 4 4 ASP ASP P . n P 1 5 ILE 5 5 5 ILE ILE P . n P 1 6 VAL 6 6 6 VAL VAL P . n P 1 7 LYS 7 7 7 LYS LYS P . n P 1 8 LYS 8 8 8 LYS LYS P . n P 1 9 ILE 9 9 9 ILE ILE P . n P 1 10 ALA 10 10 10 ALA ALA P . n P 1 11 GLY 11 11 11 GLY GLY P . n P 1 12 HIS 12 12 12 HIS HIS P . n P 1 13 ILE 13 13 13 ILE ILE P . n P 1 14 VAL 14 14 14 VAL VAL P . n P 1 15 SER 15 15 15 SER SER P . n P 1 16 SER 16 16 16 SER SER P . n P 1 17 ILE 17 17 17 ILE ILE P . n Q 1 1 GLY 1 1 1 GLY GLY O . n Q 1 2 LEU 2 2 2 LEU LEU O . n Q 1 3 PHE 3 3 3 PHE PHE O . n Q 1 4 ASP 4 4 4 ASP ASP O . n Q 1 5 ILE 5 5 5 ILE ILE O . n Q 1 6 VAL 6 6 6 VAL VAL O . n Q 1 7 LYS 7 7 7 LYS LYS O . n Q 1 8 LYS 8 8 8 LYS LYS O . n Q 1 9 ILE 9 9 9 ILE ILE O . n Q 1 10 ALA 10 10 10 ALA ALA O . n Q 1 11 GLY 11 11 11 GLY GLY O . n Q 1 12 HIS 12 12 12 HIS HIS O . n Q 1 13 ILE 13 13 13 ILE ILE O . n Q 1 14 VAL 14 14 14 VAL VAL O . n Q 1 15 SER 15 15 15 SER SER O . n Q 1 16 SER 16 16 16 SER SER O . n Q 1 17 ILE 17 17 17 ILE ILE O . n R 1 1 GLY 1 1 1 GLY GLY R . n R 1 2 LEU 2 2 2 LEU LEU R . n R 1 3 PHE 3 3 3 PHE PHE R . n R 1 4 ASP 4 4 4 ASP ASP R . n R 1 5 ILE 5 5 5 ILE ILE R . n R 1 6 VAL 6 6 6 VAL VAL R . n R 1 7 LYS 7 7 7 LYS LYS R . n R 1 8 LYS 8 8 8 LYS LYS R . n R 1 9 ILE 9 9 9 ILE ILE R . n R 1 10 ALA 10 10 10 ALA ALA R . n R 1 11 GLY 11 11 11 GLY GLY R . n R 1 12 HIS 12 12 12 HIS HIS R . n R 1 13 ILE 13 13 13 ILE ILE R . n R 1 14 VAL 14 14 14 VAL VAL R . n R 1 15 SER 15 15 15 SER SER R . n R 1 16 SER 16 16 16 SER SER R . n R 1 17 ILE 17 17 17 ILE ILE R . n # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author ? _software.contact_author_email ? _software.date ? _software.description ? _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name PHENIX _software.os ? _software.os_version ? _software.type ? _software.version 1.19.1_4122: _software.pdbx_ordinal 1 # _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 7QV6 _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 ? # _symmetry.entry_id 7QV6 _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 7QV6 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 7QV6 _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_restraint_function 'ELECTRON MICROSCOPY' ? 0.011 ? 2304 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.535 ? 3078 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 9.395 ? 306 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.054 ? 396 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.001 ? 360 ? f_plane_restr ? ? # _struct.entry_id 7QV6 _struct.title 'Amyloid fibril from the antimicrobial peptide aurein 3.3' _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 7QV6 _struct_keywords.text 'antimicrobial peptide, amyloid, filament, cross-beta, 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 ? 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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code AUR33_RANRN _struct_ref.pdbx_db_accession P82396 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GLFDIVKKIAGHIVSSI _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 7QV6 B 1 ? 17 ? P82396 1 ? 17 ? 1 17 2 1 7QV6 A 1 ? 17 ? P82396 1 ? 17 ? 1 17 3 1 7QV6 E 1 ? 17 ? P82396 1 ? 17 ? 1 17 4 1 7QV6 D 1 ? 17 ? P82396 1 ? 17 ? 1 17 5 1 7QV6 C 1 ? 17 ? P82396 1 ? 17 ? 1 17 6 1 7QV6 F 1 ? 17 ? P82396 1 ? 17 ? 1 17 7 1 7QV6 H 1 ? 17 ? P82396 1 ? 17 ? 1 17 8 1 7QV6 G 1 ? 17 ? P82396 1 ? 17 ? 1 17 9 1 7QV6 K 1 ? 17 ? P82396 1 ? 17 ? 1 17 10 1 7QV6 J 1 ? 17 ? P82396 1 ? 17 ? 1 17 11 1 7QV6 I 1 ? 17 ? P82396 1 ? 17 ? 1 17 12 1 7QV6 L 1 ? 17 ? P82396 1 ? 17 ? 1 17 13 1 7QV6 N 1 ? 17 ? P82396 1 ? 17 ? 1 17 14 1 7QV6 M 1 ? 17 ? P82396 1 ? 17 ? 1 17 15 1 7QV6 Q 1 ? 17 ? P82396 1 ? 17 ? 1 17 16 1 7QV6 P 1 ? 17 ? P82396 1 ? 17 ? 1 17 17 1 7QV6 O 1 ? 17 ? P82396 1 ? 17 ? 1 17 18 1 7QV6 R 1 ? 17 ? P82396 1 ? 17 ? 1 17 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 # _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 # _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 ? # _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 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 3 ? AA3 ? 3 ? AA4 ? 3 ? AA5 ? 3 ? AA6 ? 3 ? AA7 ? 3 ? AA8 ? 3 ? AA9 ? 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 AA4 1 2 ? parallel AA4 2 3 ? parallel AA5 1 2 ? parallel AA5 2 3 ? parallel AA6 1 2 ? parallel AA6 2 3 ? parallel AA7 1 2 ? parallel AA7 2 3 ? parallel AA8 1 2 ? parallel AA8 2 3 ? parallel AA9 1 2 ? parallel AA9 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 ? ALA A 10 ? LEU B 2 ALA B 10 AA1 2 LEU G 2 ? ALA G 10 ? LEU H 2 ALA H 10 AA1 3 LEU M 2 ? ALA M 10 ? LEU N 2 ALA N 10 AA2 1 ILE A 13 ? SER A 16 ? ILE B 13 SER B 16 AA2 2 ILE G 13 ? SER G 16 ? ILE H 13 SER H 16 AA2 3 ILE M 13 ? SER M 16 ? ILE N 13 SER N 16 AA3 1 LEU B 2 ? LYS B 8 ? LEU A 2 LYS A 8 AA3 2 LEU H 2 ? LYS H 8 ? LEU G 2 LYS G 8 AA3 3 LEU N 2 ? LYS N 8 ? LEU M 2 LYS M 8 AA4 1 ILE B 13 ? VAL B 14 ? ILE A 13 VAL A 14 AA4 2 ILE H 13 ? VAL H 14 ? ILE G 13 VAL G 14 AA4 3 ILE N 13 ? VAL N 14 ? ILE M 13 VAL M 14 AA5 1 ILE C 5 ? LYS C 7 ? ILE E 5 LYS E 7 AA5 2 ILE I 5 ? LYS I 7 ? ILE K 5 LYS K 7 AA5 3 ILE O 5 ? LYS O 7 ? ILE Q 5 LYS Q 7 AA6 1 ALA C 10 ? HIS C 12 ? ALA E 10 HIS E 12 AA6 2 ALA I 10 ? HIS I 12 ? ALA K 10 HIS K 12 AA6 3 ALA O 10 ? HIS O 12 ? ALA Q 10 HIS Q 12 AA7 1 LEU D 2 ? SER D 16 ? LEU D 2 SER D 16 AA7 2 LEU J 2 ? SER J 16 ? LEU J 2 SER J 16 AA7 3 LEU P 2 ? SER P 16 ? LEU P 2 SER P 16 AA8 1 PHE E 3 ? SER E 15 ? PHE C 3 SER C 15 AA8 2 PHE K 3 ? SER K 15 ? PHE I 3 SER I 15 AA8 3 PHE Q 3 ? SER Q 15 ? PHE O 3 SER O 15 AA9 1 PHE F 3 ? SER F 15 ? PHE F 3 SER F 15 AA9 2 PHE L 3 ? SER L 15 ? PHE L 3 SER L 15 AA9 3 PHE R 3 ? SER R 15 ? PHE R 3 SER R 15 # 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 ASP A 4 ? N ASP B 4 O PHE G 3 ? O PHE H 3 AA1 2 3 N ASP G 4 ? N ASP H 4 O PHE M 3 ? O PHE N 3 AA2 1 2 N SER A 15 ? N SER B 15 O SER G 16 ? O SER H 16 AA2 2 3 N SER G 15 ? N SER H 15 O SER M 16 ? O SER N 16 AA3 1 2 N ILE B 5 ? N ILE A 5 O VAL H 6 ? O VAL G 6 AA3 2 3 N ILE H 5 ? N ILE G 5 O VAL N 6 ? O VAL M 6 AA4 1 2 N VAL B 14 ? N VAL A 14 O ILE H 13 ? O ILE G 13 AA4 2 3 N VAL H 14 ? N VAL G 14 O ILE N 13 ? O ILE M 13 AA5 1 2 N VAL C 6 ? N VAL E 6 O ILE I 5 ? O ILE K 5 AA5 2 3 N VAL I 6 ? N VAL K 6 O ILE O 5 ? O ILE Q 5 AA6 1 2 N ALA C 10 ? N ALA E 10 O GLY I 11 ? O GLY K 11 AA6 2 3 N ALA I 10 ? N ALA K 10 O GLY O 11 ? O GLY Q 11 AA7 1 2 N SER D 15 ? N SER D 15 O SER J 16 ? O SER J 16 AA7 2 3 N SER J 15 ? N SER J 15 O SER P 16 ? O SER P 16 AA8 1 2 N PHE E 3 ? N PHE C 3 O ASP K 4 ? O ASP I 4 AA8 2 3 N PHE K 3 ? N PHE I 3 O ASP Q 4 ? O ASP O 4 AA9 1 2 N VAL F 6 ? N VAL F 6 O ILE L 5 ? O ILE L 5 AA9 2 3 N VAL L 6 ? N VAL L 6 O ILE R 5 ? O ILE R 5 # _em_3d_fitting.entry_id 7QV6 _em_3d_fitting.id 1 _em_3d_fitting.details ;- Initial model building of a single helical layer using ChimeraX and Coot - Expansion to three layers, refinement in ISOLDE - Truncation of outer layers, re-expansion to three layers, refinement using phenix.real_space_refine ; _em_3d_fitting.overall_b_value 78.37 _em_3d_fitting.ref_protocol 'FLEXIBLE FIT' _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria CC _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7QV6 _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 35289 _em_3d_reconstruction.resolution 3.5 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type HELICAL _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'aurein 3.3' _em_entity_assembly.source SYNTHETIC _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 7QV6 _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure 'ZEMLIN TABLEAU' _em_imaging.c2_aperture_diameter 70 _em_imaging.calibrated_defocus_max 3100 _em_imaging.calibrated_defocus_min 350 _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max 2500 _em_imaging.nominal_defocus_min 500 _em_imaging.nominal_magnification 105000 _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'Quantifoil R2/1' _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature 277 _em_vitrification.cryogen_name ETHANE-PROPANE _em_vitrification.details 'wait time 15s after application, blot time 4s' _em_vitrification.humidity 100 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 7QV6 _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7QV6 _em_experiment.id 1 _em_experiment.aggregation_state FILAMENT _em_experiment.reconstruction_method HELICAL _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 ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ASP N N N N 14 ASP CA C N S 15 ASP C C N N 16 ASP O O N N 17 ASP CB C N N 18 ASP CG C N N 19 ASP OD1 O N N 20 ASP OD2 O N N 21 ASP OXT O N N 22 ASP H H N N 23 ASP H2 H N N 24 ASP HA H N N 25 ASP HB2 H N N 26 ASP HB3 H N N 27 ASP HD2 H N N 28 ASP HXT H N N 29 GLY N N N N 30 GLY CA C N N 31 GLY C C N N 32 GLY O O N N 33 GLY OXT O N N 34 GLY H H N N 35 GLY H2 H N N 36 GLY HA2 H N N 37 GLY HA3 H N N 38 GLY HXT H N N 39 HIS N N N N 40 HIS CA C N S 41 HIS C C N N 42 HIS O O N N 43 HIS CB C N N 44 HIS CG C Y N 45 HIS ND1 N Y N 46 HIS CD2 C Y N 47 HIS CE1 C Y N 48 HIS NE2 N Y N 49 HIS OXT O N N 50 HIS H H N N 51 HIS H2 H N N 52 HIS HA H N N 53 HIS HB2 H N N 54 HIS HB3 H N N 55 HIS HD1 H N N 56 HIS HD2 H N N 57 HIS HE1 H N N 58 HIS HE2 H N N 59 HIS HXT H N N 60 ILE N N N N 61 ILE CA C N S 62 ILE C C N N 63 ILE O O N N 64 ILE CB C N S 65 ILE CG1 C N N 66 ILE CG2 C N N 67 ILE CD1 C N N 68 ILE OXT O N N 69 ILE H H N N 70 ILE H2 H N N 71 ILE HA H N N 72 ILE HB H N N 73 ILE HG12 H N N 74 ILE HG13 H N N 75 ILE HG21 H N N 76 ILE HG22 H N N 77 ILE HG23 H N N 78 ILE HD11 H N N 79 ILE HD12 H N N 80 ILE HD13 H N N 81 ILE HXT H N N 82 LEU N N N N 83 LEU CA C N S 84 LEU C C N N 85 LEU O O N N 86 LEU CB C N N 87 LEU CG C N N 88 LEU CD1 C N N 89 LEU CD2 C N N 90 LEU OXT O N N 91 LEU H H N N 92 LEU H2 H N N 93 LEU HA H N N 94 LEU HB2 H N N 95 LEU HB3 H N N 96 LEU HG H N N 97 LEU HD11 H N N 98 LEU HD12 H N N 99 LEU HD13 H N N 100 LEU HD21 H N N 101 LEU HD22 H N N 102 LEU HD23 H N N 103 LEU HXT H N N 104 LYS N N N N 105 LYS CA C N S 106 LYS C C N N 107 LYS O O N N 108 LYS CB C N N 109 LYS CG C N N 110 LYS CD C N N 111 LYS CE C N N 112 LYS NZ N N N 113 LYS OXT O N N 114 LYS H H N N 115 LYS H2 H N N 116 LYS HA H N N 117 LYS HB2 H N N 118 LYS HB3 H N N 119 LYS HG2 H N N 120 LYS HG3 H N N 121 LYS HD2 H N N 122 LYS HD3 H N N 123 LYS HE2 H N N 124 LYS HE3 H N N 125 LYS HZ1 H N N 126 LYS HZ2 H N N 127 LYS HZ3 H N N 128 LYS HXT H N N 129 PHE N N N N 130 PHE CA C N S 131 PHE C C N N 132 PHE O O N N 133 PHE CB C N N 134 PHE CG C Y N 135 PHE CD1 C Y N 136 PHE CD2 C Y N 137 PHE CE1 C Y N 138 PHE CE2 C Y N 139 PHE CZ C Y N 140 PHE OXT O N N 141 PHE H H N N 142 PHE H2 H N N 143 PHE HA H N N 144 PHE HB2 H N N 145 PHE HB3 H N N 146 PHE HD1 H N N 147 PHE HD2 H N N 148 PHE HE1 H N N 149 PHE HE2 H N N 150 PHE HZ H N N 151 PHE HXT H N N 152 SER N N N N 153 SER CA C N S 154 SER C C N N 155 SER O O N N 156 SER CB C N N 157 SER OG O N N 158 SER OXT O N N 159 SER H H N N 160 SER H2 H N N 161 SER HA H N N 162 SER HB2 H N N 163 SER HB3 H N N 164 SER HG H N N 165 SER HXT H N N 166 VAL N N N N 167 VAL CA C N S 168 VAL C C N N 169 VAL O O N N 170 VAL CB C N N 171 VAL CG1 C N N 172 VAL CG2 C N N 173 VAL OXT O N N 174 VAL H H N N 175 VAL H2 H N N 176 VAL HA H N N 177 VAL HB H N N 178 VAL HG11 H N N 179 VAL HG12 H N N 180 VAL HG13 H N N 181 VAL HG21 H N N 182 VAL HG22 H N N 183 VAL HG23 H N N 184 VAL HXT H N N 185 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ASP N CA sing N N 13 ASP N H sing N N 14 ASP N H2 sing N N 15 ASP CA C sing N N 16 ASP CA CB sing N N 17 ASP CA HA sing N N 18 ASP C O doub N N 19 ASP C OXT sing N N 20 ASP CB CG sing N N 21 ASP CB HB2 sing N N 22 ASP CB HB3 sing N N 23 ASP CG OD1 doub N N 24 ASP CG OD2 sing N N 25 ASP OD2 HD2 sing N N 26 ASP OXT HXT sing N N 27 GLY N CA sing N N 28 GLY N H sing N N 29 GLY N H2 sing N N 30 GLY CA C sing N N 31 GLY CA HA2 sing N N 32 GLY CA HA3 sing N N 33 GLY C O doub N N 34 GLY C OXT sing N N 35 GLY OXT HXT sing N N 36 HIS N CA sing N N 37 HIS N H sing N N 38 HIS N H2 sing N N 39 HIS CA C sing N N 40 HIS CA CB sing N N 41 HIS CA HA sing N N 42 HIS C O doub N N 43 HIS C OXT sing N N 44 HIS CB CG sing N N 45 HIS CB HB2 sing N N 46 HIS CB HB3 sing N N 47 HIS CG ND1 sing Y N 48 HIS CG CD2 doub Y N 49 HIS ND1 CE1 doub Y N 50 HIS ND1 HD1 sing N N 51 HIS CD2 NE2 sing Y N 52 HIS CD2 HD2 sing N N 53 HIS CE1 NE2 sing Y N 54 HIS CE1 HE1 sing N N 55 HIS NE2 HE2 sing N N 56 HIS OXT HXT sing N N 57 ILE N CA sing N N 58 ILE N H sing N N 59 ILE N H2 sing N N 60 ILE CA C sing N N 61 ILE CA CB sing N N 62 ILE CA HA sing N N 63 ILE C O doub N N 64 ILE C OXT sing N N 65 ILE CB CG1 sing N N 66 ILE CB CG2 sing N N 67 ILE CB HB sing N N 68 ILE CG1 CD1 sing N N 69 ILE CG1 HG12 sing N N 70 ILE CG1 HG13 sing N N 71 ILE CG2 HG21 sing N N 72 ILE CG2 HG22 sing N N 73 ILE CG2 HG23 sing N N 74 ILE CD1 HD11 sing N N 75 ILE CD1 HD12 sing N N 76 ILE CD1 HD13 sing N N 77 ILE OXT HXT sing N N 78 LEU N CA sing N N 79 LEU N H sing N N 80 LEU N H2 sing N N 81 LEU CA C sing N N 82 LEU CA CB sing N N 83 LEU CA HA sing N N 84 LEU C O doub N N 85 LEU C OXT sing N N 86 LEU CB CG sing N N 87 LEU CB HB2 sing N N 88 LEU CB HB3 sing N N 89 LEU CG CD1 sing N N 90 LEU CG CD2 sing N N 91 LEU CG HG sing N N 92 LEU CD1 HD11 sing N N 93 LEU CD1 HD12 sing N N 94 LEU CD1 HD13 sing N N 95 LEU CD2 HD21 sing N N 96 LEU CD2 HD22 sing N N 97 LEU CD2 HD23 sing N N 98 LEU OXT HXT sing N N 99 LYS N CA sing N N 100 LYS N H sing N N 101 LYS N H2 sing N N 102 LYS CA C sing N N 103 LYS CA CB sing N N 104 LYS CA HA sing N N 105 LYS C O doub N N 106 LYS C OXT sing N N 107 LYS CB CG sing N N 108 LYS CB HB2 sing N N 109 LYS CB HB3 sing N N 110 LYS CG CD sing N N 111 LYS CG HG2 sing N N 112 LYS CG HG3 sing N N 113 LYS CD CE sing N N 114 LYS CD HD2 sing N N 115 LYS CD HD3 sing N N 116 LYS CE NZ sing N N 117 LYS CE HE2 sing N N 118 LYS CE HE3 sing N N 119 LYS NZ HZ1 sing N N 120 LYS NZ HZ2 sing N N 121 LYS NZ HZ3 sing N N 122 LYS OXT HXT sing N N 123 PHE N CA sing N N 124 PHE N H sing N N 125 PHE N H2 sing N N 126 PHE CA C sing N N 127 PHE CA CB sing N N 128 PHE CA HA sing N N 129 PHE C O doub N N 130 PHE C OXT sing N N 131 PHE CB CG sing N N 132 PHE CB HB2 sing N N 133 PHE CB HB3 sing N N 134 PHE CG CD1 doub Y N 135 PHE CG CD2 sing Y N 136 PHE CD1 CE1 sing Y N 137 PHE CD1 HD1 sing N N 138 PHE CD2 CE2 doub Y N 139 PHE CD2 HD2 sing N N 140 PHE CE1 CZ doub Y N 141 PHE CE1 HE1 sing N N 142 PHE CE2 CZ sing Y N 143 PHE CE2 HE2 sing N N 144 PHE CZ HZ sing N N 145 PHE OXT HXT sing N N 146 SER N CA sing N N 147 SER N H sing N N 148 SER N H2 sing N N 149 SER CA C sing N N 150 SER CA CB sing N N 151 SER CA HA sing N N 152 SER C O doub N N 153 SER C OXT sing N N 154 SER CB OG sing N N 155 SER CB HB2 sing N N 156 SER CB HB3 sing N N 157 SER OG HG sing N N 158 SER OXT HXT sing N N 159 VAL N CA sing N N 160 VAL N H sing N N 161 VAL N H2 sing N N 162 VAL CA C sing N N 163 VAL CA CB sing N N 164 VAL CA HA sing N N 165 VAL C O doub N N 166 VAL C OXT sing N N 167 VAL CB CG1 sing N N 168 VAL CB CG2 sing N N 169 VAL CB HB sing N N 170 VAL CG1 HG11 sing N N 171 VAL CG1 HG12 sing N N 172 VAL CG1 HG13 sing N N 173 VAL CG2 HG21 sing N N 174 VAL CG2 HG22 sing N N 175 VAL CG2 HG23 sing N N 176 VAL OXT HXT sing N N 177 # _em_admin.entry_id 7QV6 _em_admin.current_status REL _em_admin.deposition_date 2022-01-19 _em_admin.deposition_site PDBE _em_admin.last_update 2024-07-17 _em_admin.map_release_date 2022-06-29 _em_admin.title 'Amyloid fibril from the antimicrobial peptide aurein 3.3' # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details 'CTF refined after 3D reconstruction' # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units KILODALTONS/NANOMETER _em_entity_assembly_molwt.value 22.3 # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.ncbi_tax_id 116057 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Ranoidea raniformis' _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 1 _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.angular_rotation_per_subunit -1.136 _em_helical_entity.axial_rise_per_subunit 4.892 _em_helical_entity.axial_symmetry C1 _em_helical_entity.details ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 40 _em_image_recording.average_exposure_time 2 _em_image_recording.details 'Collected in movie-mode; 40 frames per exposure.' _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 BIOQUANTUM (6k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged 1 _em_image_recording.num_real_images 5514 _em_image_recording.avg_electron_dose_per_subtomogram ? # _em_imaging_optics.id 1 _em_imaging_optics.imaging_id 1 _em_imaging_optics.chr_aberration_corrector ? _em_imaging_optics.energyfilter_lower ? _em_imaging_optics.energyfilter_name 'GIF Bioquantum' _em_imaging_optics.energyfilter_upper ? _em_imaging_optics.energyfilter_slit_width 15 _em_imaging_optics.phase_plate ? _em_imaging_optics.sph_aberration_corrector ? _em_imaging_optics.details ? # _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.details '4 unique helical units per segment' _em_particle_selection.method ? _em_particle_selection.num_particles_selected 174291 _em_particle_selection.reference_model ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 1 1 2 'IMAGE ACQUISITION' ? EPU 2.8.0.1256 ? ? 1 3 'IMAGE ACQUISITION' ? DigitalMicrograph 3.32.2403 ? ? 1 4 MASKING ? ? ? ? ? ? 5 'CTF CORRECTION' 'Internal CTFFIND4' RELION 3.1.3 1 ? ? 6 'LAYERLINE INDEXING' ? ? ? ? ? ? 7 'DIFFRACTION INDEXING' ? ? ? ? ? ? 8 'MODEL FITTING' ? 'UCSF ChimeraX' 1.3 ? 1 ? 9 'MODEL FITTING' ? Coot 0.9.3 ? 1 ? 10 OTHER ? ? ? ? ? ? 11 'INITIAL EULER ASSIGNMENT' 'Helical SGD initial model' cryoSPARC 2.3 1 ? ? 12 'INITIAL EULER ASSIGNMENT' '2D classes for helical parameter estimation' RELION 3.1.3 1 ? ? 13 'FINAL EULER ASSIGNMENT' ? RELION 3.1.3 1 ? ? 14 CLASSIFICATION ? RELION 3.1.3 1 ? ? 15 RECONSTRUCTION ? RELION 3.1.3 1 ? ? 16 'MODEL REFINEMENT' ? PHENIX 1.19.1 ? 1 ? 17 'MODEL REFINEMENT' ? ISOLDE 1.0 ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 5 _em_specimen.details 'Concentration refers to peptide monomer before fibrillation' _em_specimen.embedding_applied NO _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 'Other government' ? LOM2018 1 'Israel Science Foundation' ? 2111/20 2 'Israel Ministry of Science and Technology' ? 3-15517 3 'United States - Israel Binational Science Foundation (BSF)' ? 2017280 4 'Joachim Herz Stiftung' ? 'Add-on Fellowship' 5 # _atom_sites.entry_id 7QV6 _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 H N O # loop_