data_9K0E # _entry.id 9K0E # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.404 _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 9K0E pdb_00009k0e 10.2210/pdb9k0e/pdb WWPDB D_1300052637 ? ? EMDB EMD-61945 ? ? # _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 2025-08-06 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9K0E _pdbx_database_status.recvd_initial_deposition_date 2024-10-15 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 Amyloid-beta42-4b polymorph 2' _pdbx_database_related.db_id EMD-61945 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email xiawc@sioc.ac.cn _pdbx_contact_author.name_first Cong _pdbx_contact_author.name_last Liu _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-3425-6672 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Xia, W.C.' 1 ? 'Sun, Y.P.' 2 ? 'Liu, C.' 3 ? # _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 16 _citation.language ? _citation.page_first 5815 _citation.page_last 5815 _citation.title 'An O-glycopeptide participates in the formation of distinct A beta 42 fibril structures and attenuates A beta 42 neurotoxicity.' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-025-60978-w _citation.pdbx_database_id_PubMed 40593714 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wei, Q.' 1 0000-0002-1633-9880 primary 'Liu, D.' 2 ? primary 'Xia, W.' 3 ? primary 'Wang, F.' 4 ? primary 'Huang, L.' 5 0000-0002-1211-5441 primary 'Zhang, J.' 6 ? primary 'Wang, X.' 7 0000-0002-7500-2428 primary 'Xu, Z.' 8 ? primary 'He, C.' 9 0000-0002-5807-6177 primary 'Li, W.' 10 0000-0002-5607-5509 primary 'Shi, X.' 11 ? primary 'Wang, C.' 12 0000-0002-6925-1268 primary 'Liu, Y.' 13 0000-0002-1156-7673 primary 'Liu, C.' 14 0000-0003-3425-6672 primary 'Dong, S.' 15 0000-0002-2648-4344 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Amyloid-beta A4 protein' 4520.087 6 ? ? ? ? 2 polymer syn 'Amyloid-beta protein 40' 1577.802 6 ? ? ? ? 3 water nat water 18.015 6 ? ? ? ? # _entity_name_com.entity_id 2 _entity_name_com.name Abeta40,Beta-APP40 # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA G,B,N,H,O,I ? 2 'polypeptide(L)' no no GYEVHHQKLVFFA GYEVHHQKLVFFA F,A,L,D,M,E ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASP n 1 2 ALA n 1 3 GLU n 1 4 PHE n 1 5 ARG n 1 6 HIS n 1 7 ASP n 1 8 SER n 1 9 GLY n 1 10 TYR n 1 11 GLU n 1 12 VAL n 1 13 HIS n 1 14 HIS n 1 15 GLN n 1 16 LYS n 1 17 LEU n 1 18 VAL n 1 19 PHE n 1 20 PHE n 1 21 ALA n 1 22 GLU n 1 23 ASP n 1 24 VAL n 1 25 GLY n 1 26 SER n 1 27 ASN n 1 28 LYS n 1 29 GLY n 1 30 ALA n 1 31 ILE n 1 32 ILE n 1 33 GLY n 1 34 LEU n 1 35 MET n 1 36 VAL n 1 37 GLY n 1 38 GLY n 1 39 VAL n 1 40 VAL n 1 41 ILE n 1 42 ALA n 2 1 GLY n 2 2 TYR n 2 3 GLU n 2 4 VAL n 2 5 HIS n 2 6 HIS n 2 7 GLN n 2 8 LYS n 2 9 LEU n 2 10 VAL n 2 11 PHE n 2 12 PHE n 2 13 ALA n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 42 'Homo sapiens' human 9606 ? 2 1 sample 1 13 'Homo sapiens' human 9606 ? # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 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 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 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 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 ASP 1 1 ? ? ? G . n A 1 2 ALA 2 2 ? ? ? G . n A 1 3 GLU 3 3 ? ? ? G . n A 1 4 PHE 4 4 ? ? ? G . n A 1 5 ARG 5 5 ? ? ? G . n A 1 6 HIS 6 6 ? ? ? G . n A 1 7 ASP 7 7 ? ? ? G . n A 1 8 SER 8 8 ? ? ? G . n A 1 9 GLY 9 9 ? ? ? G . n A 1 10 TYR 10 10 ? ? ? G . n A 1 11 GLU 11 11 11 GLU GLU G . n A 1 12 VAL 12 12 12 VAL VAL G . n A 1 13 HIS 13 13 13 HIS HIS G . n A 1 14 HIS 14 14 14 HIS HIS G . n A 1 15 GLN 15 15 15 GLN GLN G . n A 1 16 LYS 16 16 16 LYS LYS G . n A 1 17 LEU 17 17 17 LEU LEU G . n A 1 18 VAL 18 18 18 VAL VAL G . n A 1 19 PHE 19 19 19 PHE PHE G . n A 1 20 PHE 20 20 20 PHE PHE G . n A 1 21 ALA 21 21 21 ALA ALA G . n A 1 22 GLU 22 22 22 GLU GLU G . n A 1 23 ASP 23 23 23 ASP ASP G . n A 1 24 VAL 24 24 24 VAL VAL G . n A 1 25 GLY 25 25 25 GLY GLY G . n A 1 26 SER 26 26 26 SER SER G . n A 1 27 ASN 27 27 27 ASN ASN G . n A 1 28 LYS 28 28 28 LYS LYS G . n A 1 29 GLY 29 29 29 GLY GLY G . n A 1 30 ALA 30 30 30 ALA ALA G . n A 1 31 ILE 31 31 31 ILE ILE G . n A 1 32 ILE 32 32 32 ILE ILE G . n A 1 33 GLY 33 33 33 GLY GLY G . n A 1 34 LEU 34 34 34 LEU LEU G . n A 1 35 MET 35 35 35 MET MET G . n A 1 36 VAL 36 36 36 VAL VAL G . n A 1 37 GLY 37 37 37 GLY GLY G . n A 1 38 GLY 38 38 38 GLY GLY G . n A 1 39 VAL 39 39 39 VAL VAL G . n A 1 40 VAL 40 40 40 VAL VAL G . n A 1 41 ILE 41 41 41 ILE ILE G . n A 1 42 ALA 42 42 42 ALA ALA G . n B 2 1 GLY 1 9 ? ? ? F . n B 2 2 TYR 2 10 ? ? ? F . n B 2 3 GLU 3 11 11 GLU GLU F . n B 2 4 VAL 4 12 12 VAL VAL F . n B 2 5 HIS 5 13 13 HIS HIS F . n B 2 6 HIS 6 14 14 HIS HIS F . n B 2 7 GLN 7 15 15 GLN GLN F . n B 2 8 LYS 8 16 16 LYS LYS F . n B 2 9 LEU 9 17 17 LEU LEU F . n B 2 10 VAL 10 18 18 VAL VAL F . n B 2 11 PHE 11 19 19 PHE PHE F . n B 2 12 PHE 12 20 ? ? ? F . n B 2 13 ALA 13 21 ? ? ? F . n C 1 1 ASP 1 1 ? ? ? B . n C 1 2 ALA 2 2 ? ? ? B . n C 1 3 GLU 3 3 ? ? ? B . n C 1 4 PHE 4 4 ? ? ? B . n C 1 5 ARG 5 5 ? ? ? B . n C 1 6 HIS 6 6 ? ? ? B . n C 1 7 ASP 7 7 ? ? ? B . n C 1 8 SER 8 8 ? ? ? B . n C 1 9 GLY 9 9 ? ? ? B . n C 1 10 TYR 10 10 ? ? ? B . n C 1 11 GLU 11 11 11 GLU GLU B . n C 1 12 VAL 12 12 12 VAL VAL B . n C 1 13 HIS 13 13 13 HIS HIS B . n C 1 14 HIS 14 14 14 HIS HIS B . n C 1 15 GLN 15 15 15 GLN GLN B . n C 1 16 LYS 16 16 16 LYS LYS B . n C 1 17 LEU 17 17 17 LEU LEU B . n C 1 18 VAL 18 18 18 VAL VAL B . n C 1 19 PHE 19 19 19 PHE PHE B . n C 1 20 PHE 20 20 20 PHE PHE B . n C 1 21 ALA 21 21 21 ALA ALA B . n C 1 22 GLU 22 22 22 GLU GLU B . n C 1 23 ASP 23 23 23 ASP ASP B . n C 1 24 VAL 24 24 24 VAL VAL B . n C 1 25 GLY 25 25 25 GLY GLY B . n C 1 26 SER 26 26 26 SER SER B . n C 1 27 ASN 27 27 27 ASN ASN B . n C 1 28 LYS 28 28 28 LYS LYS B . n C 1 29 GLY 29 29 29 GLY GLY B . n C 1 30 ALA 30 30 30 ALA ALA B . n C 1 31 ILE 31 31 31 ILE ILE B . n C 1 32 ILE 32 32 32 ILE ILE B . n C 1 33 GLY 33 33 33 GLY GLY B . n C 1 34 LEU 34 34 34 LEU LEU B . n C 1 35 MET 35 35 35 MET MET B . n C 1 36 VAL 36 36 36 VAL VAL B . n C 1 37 GLY 37 37 37 GLY GLY B . n C 1 38 GLY 38 38 38 GLY GLY B . n C 1 39 VAL 39 39 39 VAL VAL B . n C 1 40 VAL 40 40 40 VAL VAL B . n C 1 41 ILE 41 41 41 ILE ILE B . n C 1 42 ALA 42 42 42 ALA ALA B . n D 2 1 GLY 1 9 ? ? ? A . n D 2 2 TYR 2 10 ? ? ? A . n D 2 3 GLU 3 11 11 GLU GLU A . n D 2 4 VAL 4 12 12 VAL VAL A . n D 2 5 HIS 5 13 13 HIS HIS A . n D 2 6 HIS 6 14 14 HIS HIS A . n D 2 7 GLN 7 15 15 GLN GLN A . n D 2 8 LYS 8 16 16 LYS LYS A . n D 2 9 LEU 9 17 17 LEU LEU A . n D 2 10 VAL 10 18 18 VAL VAL A . n D 2 11 PHE 11 19 19 PHE PHE A . n D 2 12 PHE 12 20 ? ? ? A . n D 2 13 ALA 13 21 ? ? ? A . n E 1 1 ASP 1 1 ? ? ? N . n E 1 2 ALA 2 2 ? ? ? N . n E 1 3 GLU 3 3 ? ? ? N . n E 1 4 PHE 4 4 ? ? ? N . n E 1 5 ARG 5 5 ? ? ? N . n E 1 6 HIS 6 6 ? ? ? N . n E 1 7 ASP 7 7 ? ? ? N . n E 1 8 SER 8 8 ? ? ? N . n E 1 9 GLY 9 9 ? ? ? N . n E 1 10 TYR 10 10 ? ? ? N . n E 1 11 GLU 11 11 11 GLU GLU N . n E 1 12 VAL 12 12 12 VAL VAL N . n E 1 13 HIS 13 13 13 HIS HIS N . n E 1 14 HIS 14 14 14 HIS HIS N . n E 1 15 GLN 15 15 15 GLN GLN N . n E 1 16 LYS 16 16 16 LYS LYS N . n E 1 17 LEU 17 17 17 LEU LEU N . n E 1 18 VAL 18 18 18 VAL VAL N . n E 1 19 PHE 19 19 19 PHE PHE N . n E 1 20 PHE 20 20 20 PHE PHE N . n E 1 21 ALA 21 21 21 ALA ALA N . n E 1 22 GLU 22 22 22 GLU GLU N . n E 1 23 ASP 23 23 23 ASP ASP N . n E 1 24 VAL 24 24 24 VAL VAL N . n E 1 25 GLY 25 25 25 GLY GLY N . n E 1 26 SER 26 26 26 SER SER N . n E 1 27 ASN 27 27 27 ASN ASN N . n E 1 28 LYS 28 28 28 LYS LYS N . n E 1 29 GLY 29 29 29 GLY GLY N . n E 1 30 ALA 30 30 30 ALA ALA N . n E 1 31 ILE 31 31 31 ILE ILE N . n E 1 32 ILE 32 32 32 ILE ILE N . n E 1 33 GLY 33 33 33 GLY GLY N . n E 1 34 LEU 34 34 34 LEU LEU N . n E 1 35 MET 35 35 35 MET MET N . n E 1 36 VAL 36 36 36 VAL VAL N . n E 1 37 GLY 37 37 37 GLY GLY N . n E 1 38 GLY 38 38 38 GLY GLY N . n E 1 39 VAL 39 39 39 VAL VAL N . n E 1 40 VAL 40 40 40 VAL VAL N . n E 1 41 ILE 41 41 41 ILE ILE N . n E 1 42 ALA 42 42 42 ALA ALA N . n F 2 1 GLY 1 9 ? ? ? L . n F 2 2 TYR 2 10 ? ? ? L . n F 2 3 GLU 3 11 11 GLU GLU L . n F 2 4 VAL 4 12 12 VAL VAL L . n F 2 5 HIS 5 13 13 HIS HIS L . n F 2 6 HIS 6 14 14 HIS HIS L . n F 2 7 GLN 7 15 15 GLN GLN L . n F 2 8 LYS 8 16 16 LYS LYS L . n F 2 9 LEU 9 17 17 LEU LEU L . n F 2 10 VAL 10 18 18 VAL VAL L . n F 2 11 PHE 11 19 19 PHE PHE L . n F 2 12 PHE 12 20 ? ? ? L . n F 2 13 ALA 13 21 ? ? ? L . n G 1 1 ASP 1 1 ? ? ? H . n G 1 2 ALA 2 2 ? ? ? H . n G 1 3 GLU 3 3 ? ? ? H . n G 1 4 PHE 4 4 ? ? ? H . n G 1 5 ARG 5 5 ? ? ? H . n G 1 6 HIS 6 6 ? ? ? H . n G 1 7 ASP 7 7 ? ? ? H . n G 1 8 SER 8 8 ? ? ? H . n G 1 9 GLY 9 9 ? ? ? H . n G 1 10 TYR 10 10 ? ? ? H . n G 1 11 GLU 11 11 11 GLU GLU H . n G 1 12 VAL 12 12 12 VAL VAL H . n G 1 13 HIS 13 13 13 HIS HIS H . n G 1 14 HIS 14 14 14 HIS HIS H . n G 1 15 GLN 15 15 15 GLN GLN H . n G 1 16 LYS 16 16 16 LYS LYS H . n G 1 17 LEU 17 17 17 LEU LEU H . n G 1 18 VAL 18 18 18 VAL VAL H . n G 1 19 PHE 19 19 19 PHE PHE H . n G 1 20 PHE 20 20 20 PHE PHE H . n G 1 21 ALA 21 21 21 ALA ALA H . n G 1 22 GLU 22 22 22 GLU GLU H . n G 1 23 ASP 23 23 23 ASP ASP H . n G 1 24 VAL 24 24 24 VAL VAL H . n G 1 25 GLY 25 25 25 GLY GLY H . n G 1 26 SER 26 26 26 SER SER H . n G 1 27 ASN 27 27 27 ASN ASN H . n G 1 28 LYS 28 28 28 LYS LYS H . n G 1 29 GLY 29 29 29 GLY GLY H . n G 1 30 ALA 30 30 30 ALA ALA H . n G 1 31 ILE 31 31 31 ILE ILE H . n G 1 32 ILE 32 32 32 ILE ILE H . n G 1 33 GLY 33 33 33 GLY GLY H . n G 1 34 LEU 34 34 34 LEU LEU H . n G 1 35 MET 35 35 35 MET MET H . n G 1 36 VAL 36 36 36 VAL VAL H . n G 1 37 GLY 37 37 37 GLY GLY H . n G 1 38 GLY 38 38 38 GLY GLY H . n G 1 39 VAL 39 39 39 VAL VAL H . n G 1 40 VAL 40 40 40 VAL VAL H . n G 1 41 ILE 41 41 41 ILE ILE H . n G 1 42 ALA 42 42 42 ALA ALA H . n H 2 1 GLY 1 9 ? ? ? D . n H 2 2 TYR 2 10 ? ? ? D . n H 2 3 GLU 3 11 11 GLU GLU D . n H 2 4 VAL 4 12 12 VAL VAL D . n H 2 5 HIS 5 13 13 HIS HIS D . n H 2 6 HIS 6 14 14 HIS HIS D . n H 2 7 GLN 7 15 15 GLN GLN D . n H 2 8 LYS 8 16 16 LYS LYS D . n H 2 9 LEU 9 17 17 LEU LEU D . n H 2 10 VAL 10 18 18 VAL VAL D . n H 2 11 PHE 11 19 19 PHE PHE D . n H 2 12 PHE 12 20 ? ? ? D . n H 2 13 ALA 13 21 ? ? ? D . n I 1 1 ASP 1 1 ? ? ? O . n I 1 2 ALA 2 2 ? ? ? O . n I 1 3 GLU 3 3 ? ? ? O . n I 1 4 PHE 4 4 ? ? ? O . n I 1 5 ARG 5 5 ? ? ? O . n I 1 6 HIS 6 6 ? ? ? O . n I 1 7 ASP 7 7 ? ? ? O . n I 1 8 SER 8 8 ? ? ? O . n I 1 9 GLY 9 9 ? ? ? O . n I 1 10 TYR 10 10 ? ? ? O . n I 1 11 GLU 11 11 11 GLU GLU O . n I 1 12 VAL 12 12 12 VAL VAL O . n I 1 13 HIS 13 13 13 HIS HIS O . n I 1 14 HIS 14 14 14 HIS HIS O . n I 1 15 GLN 15 15 15 GLN GLN O . n I 1 16 LYS 16 16 16 LYS LYS O . n I 1 17 LEU 17 17 17 LEU LEU O . n I 1 18 VAL 18 18 18 VAL VAL O . n I 1 19 PHE 19 19 19 PHE PHE O . n I 1 20 PHE 20 20 20 PHE PHE O . n I 1 21 ALA 21 21 21 ALA ALA O . n I 1 22 GLU 22 22 22 GLU GLU O . n I 1 23 ASP 23 23 23 ASP ASP O . n I 1 24 VAL 24 24 24 VAL VAL O . n I 1 25 GLY 25 25 25 GLY GLY O . n I 1 26 SER 26 26 26 SER SER O . n I 1 27 ASN 27 27 27 ASN ASN O . n I 1 28 LYS 28 28 28 LYS LYS O . n I 1 29 GLY 29 29 29 GLY GLY O . n I 1 30 ALA 30 30 30 ALA ALA O . n I 1 31 ILE 31 31 31 ILE ILE O . n I 1 32 ILE 32 32 32 ILE ILE O . n I 1 33 GLY 33 33 33 GLY GLY O . n I 1 34 LEU 34 34 34 LEU LEU O . n I 1 35 MET 35 35 35 MET MET O . n I 1 36 VAL 36 36 36 VAL VAL O . n I 1 37 GLY 37 37 37 GLY GLY O . n I 1 38 GLY 38 38 38 GLY GLY O . n I 1 39 VAL 39 39 39 VAL VAL O . n I 1 40 VAL 40 40 40 VAL VAL O . n I 1 41 ILE 41 41 41 ILE ILE O . n I 1 42 ALA 42 42 42 ALA ALA O . n J 2 1 GLY 1 9 ? ? ? M . n J 2 2 TYR 2 10 ? ? ? M . n J 2 3 GLU 3 11 11 GLU GLU M . n J 2 4 VAL 4 12 12 VAL VAL M . n J 2 5 HIS 5 13 13 HIS HIS M . n J 2 6 HIS 6 14 14 HIS HIS M . n J 2 7 GLN 7 15 15 GLN GLN M . n J 2 8 LYS 8 16 16 LYS LYS M . n J 2 9 LEU 9 17 17 LEU LEU M . n J 2 10 VAL 10 18 18 VAL VAL M . n J 2 11 PHE 11 19 19 PHE PHE M . n J 2 12 PHE 12 20 ? ? ? M . n J 2 13 ALA 13 21 ? ? ? M . n K 1 1 ASP 1 1 ? ? ? I . n K 1 2 ALA 2 2 ? ? ? I . n K 1 3 GLU 3 3 ? ? ? I . n K 1 4 PHE 4 4 ? ? ? I . n K 1 5 ARG 5 5 ? ? ? I . n K 1 6 HIS 6 6 ? ? ? I . n K 1 7 ASP 7 7 ? ? ? I . n K 1 8 SER 8 8 ? ? ? I . n K 1 9 GLY 9 9 ? ? ? I . n K 1 10 TYR 10 10 ? ? ? I . n K 1 11 GLU 11 11 11 GLU GLU I . n K 1 12 VAL 12 12 12 VAL VAL I . n K 1 13 HIS 13 13 13 HIS HIS I . n K 1 14 HIS 14 14 14 HIS HIS I . n K 1 15 GLN 15 15 15 GLN GLN I . n K 1 16 LYS 16 16 16 LYS LYS I . n K 1 17 LEU 17 17 17 LEU LEU I . n K 1 18 VAL 18 18 18 VAL VAL I . n K 1 19 PHE 19 19 19 PHE PHE I . n K 1 20 PHE 20 20 20 PHE PHE I . n K 1 21 ALA 21 21 21 ALA ALA I . n K 1 22 GLU 22 22 22 GLU GLU I . n K 1 23 ASP 23 23 23 ASP ASP I . n K 1 24 VAL 24 24 24 VAL VAL I . n K 1 25 GLY 25 25 25 GLY GLY I . n K 1 26 SER 26 26 26 SER SER I . n K 1 27 ASN 27 27 27 ASN ASN I . n K 1 28 LYS 28 28 28 LYS LYS I . n K 1 29 GLY 29 29 29 GLY GLY I . n K 1 30 ALA 30 30 30 ALA ALA I . n K 1 31 ILE 31 31 31 ILE ILE I . n K 1 32 ILE 32 32 32 ILE ILE I . n K 1 33 GLY 33 33 33 GLY GLY I . n K 1 34 LEU 34 34 34 LEU LEU I . n K 1 35 MET 35 35 35 MET MET I . n K 1 36 VAL 36 36 36 VAL VAL I . n K 1 37 GLY 37 37 37 GLY GLY I . n K 1 38 GLY 38 38 38 GLY GLY I . n K 1 39 VAL 39 39 39 VAL VAL I . n K 1 40 VAL 40 40 40 VAL VAL I . n K 1 41 ILE 41 41 41 ILE ILE I . n K 1 42 ALA 42 42 42 ALA ALA I . n L 2 1 GLY 1 9 ? ? ? E . n L 2 2 TYR 2 10 ? ? ? E . n L 2 3 GLU 3 11 11 GLU GLU E . n L 2 4 VAL 4 12 12 VAL VAL E . n L 2 5 HIS 5 13 13 HIS HIS E . n L 2 6 HIS 6 14 14 HIS HIS E . n L 2 7 GLN 7 15 15 GLN GLN E . n L 2 8 LYS 8 16 16 LYS LYS E . n L 2 9 LEU 9 17 17 LEU LEU E . n L 2 10 VAL 10 18 18 VAL VAL E . n L 2 11 PHE 11 19 19 PHE PHE E . n L 2 12 PHE 12 20 ? ? ? E . n L 2 13 ALA 13 21 ? ? ? E . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code M 3 HOH 1 101 3 HOH HOH G . N 3 HOH 1 101 2 HOH HOH B . O 3 HOH 1 101 3 HOH HOH N . O 3 HOH 2 102 3 HOH HOH N . P 3 HOH 1 101 2 HOH HOH H . P 3 HOH 2 102 2 HOH HOH H . # _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 9K0E _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9K0E _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 9K0E _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9K0E _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high . _refine.ls_d_res_low ? _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work ? _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.006 ? 1914 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.644 ? 2562 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 12.851 ? 1080 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.056 ? 300 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.003 ? 318 ? f_plane_restr ? ? # _struct.entry_id 9K0E _struct.title 'Cryo-EM structure of Amyloid-beta42-4b 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 9K0E _struct_keywords.text 'helical fibril, amyloid-beta, PROTEIN FIBRIL, MEMBRANE PROTEIN' _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN' # 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 2 ? C N N 1 ? D N N 2 ? E N N 1 ? F N N 2 ? G N N 1 ? H N N 2 ? I N N 1 ? J N N 2 ? K N N 1 ? L N N 2 ? M N N 3 ? N N N 3 ? O N N 3 ? P N N 3 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 UNP B4DMD5_HUMAN B4DMD5 ? 1 DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA 524 2 UNP A4_HUMAN P05067 ? 2 GYEVHHQKLVFFA 680 # 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 9K0E G 1 ? 42 ? B4DMD5 524 ? 565 ? 1 42 2 2 9K0E F 1 ? 13 ? P05067 680 ? 692 ? 9 21 3 1 9K0E B 1 ? 42 ? B4DMD5 524 ? 565 ? 1 42 4 2 9K0E A 1 ? 13 ? P05067 680 ? 692 ? 9 21 5 1 9K0E N 1 ? 42 ? B4DMD5 524 ? 565 ? 1 42 6 2 9K0E L 1 ? 13 ? P05067 680 ? 692 ? 9 21 7 1 9K0E H 1 ? 42 ? B4DMD5 524 ? 565 ? 1 42 8 2 9K0E D 1 ? 13 ? P05067 680 ? 692 ? 9 21 9 1 9K0E O 1 ? 42 ? B4DMD5 524 ? 565 ? 1 42 10 2 9K0E M 1 ? 13 ? P05067 680 ? 692 ? 9 21 11 1 9K0E I 1 ? 42 ? B4DMD5 524 ? 565 ? 1 42 12 2 9K0E E 1 ? 13 ? P05067 680 ? 692 ? 9 21 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 12-meric _pdbx_struct_assembly.oligomeric_count 12 # _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 # _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 ? AA4 ? 3 ? AA5 ? 3 ? AA6 ? 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 # 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 ILE E 31 ? GLY E 33 ? ILE N 31 GLY N 33 AA1 2 ILE A 31 ? GLY A 33 ? ILE G 31 GLY G 33 AA1 3 ILE I 31 ? GLY I 33 ? ILE O 31 GLY O 33 AA2 1 VAL E 39 ? ILE E 41 ? VAL N 39 ILE N 41 AA2 2 VAL A 39 ? ILE A 41 ? VAL G 39 ILE G 41 AA2 3 VAL I 39 ? ILE I 41 ? VAL O 39 ILE O 41 AA3 1 VAL F 4 ? HIS F 5 ? VAL L 12 HIS L 13 AA3 2 VAL B 4 ? GLN B 7 ? VAL F 12 GLN F 15 AA3 3 VAL J 4 ? GLN J 7 ? VAL M 12 GLN M 15 AA4 1 ILE G 31 ? GLY G 33 ? ILE H 31 GLY H 33 AA4 2 ILE C 31 ? GLY C 33 ? ILE B 31 GLY B 33 AA4 3 ILE K 31 ? GLY K 33 ? ILE I 31 GLY I 33 AA5 1 VAL G 39 ? ILE G 41 ? VAL H 39 ILE H 41 AA5 2 VAL C 39 ? ILE C 41 ? VAL B 39 ILE B 41 AA5 3 VAL K 39 ? ILE K 41 ? VAL I 39 ILE I 41 AA6 1 VAL H 4 ? HIS H 5 ? VAL D 12 HIS D 13 AA6 2 VAL D 4 ? GLN D 7 ? VAL A 12 GLN A 15 AA6 3 VAL L 4 ? GLN L 7 ? VAL E 12 GLN E 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 O ILE E 32 ? O ILE N 32 N ILE A 31 ? N ILE G 31 AA1 2 3 N ILE A 32 ? N ILE G 32 O ILE I 31 ? O ILE O 31 AA2 1 2 O ILE E 41 ? O ILE N 41 N VAL A 40 ? N VAL G 40 AA2 2 3 N ILE A 41 ? N ILE G 41 O VAL I 40 ? O VAL O 40 AA3 1 2 O HIS F 5 ? O HIS L 13 N VAL B 4 ? N VAL F 12 AA3 2 3 N HIS B 5 ? N HIS F 13 O VAL J 4 ? O VAL M 12 AA4 1 2 O ILE G 32 ? O ILE H 32 N ILE C 31 ? N ILE B 31 AA4 2 3 N ILE C 32 ? N ILE B 32 O ILE K 31 ? O ILE I 31 AA5 1 2 O ILE G 41 ? O ILE H 41 N VAL C 40 ? N VAL B 40 AA5 2 3 N ILE C 41 ? N ILE B 41 O VAL K 40 ? O VAL I 40 AA6 1 2 O HIS H 5 ? O HIS D 13 N VAL D 4 ? N VAL A 12 AA6 2 3 N HIS D 5 ? N HIS A 13 O VAL L 4 ? O VAL E 12 # _pdbx_entry_details.entry_id 9K0E _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 GLN G 15 ? ? -164.28 117.27 2 1 ALA G 21 ? ? -102.76 -60.32 3 1 GLU G 22 ? ? -103.28 -167.58 4 1 ASP G 23 ? ? -69.28 73.03 5 1 GLN B 15 ? ? -164.27 117.22 6 1 ALA B 21 ? ? -102.63 -60.29 7 1 GLU B 22 ? ? -103.36 -167.54 8 1 ASP B 23 ? ? -69.35 73.05 9 1 GLN N 15 ? ? -164.26 117.25 10 1 ALA N 21 ? ? -102.73 -60.31 11 1 GLU N 22 ? ? -103.37 -167.53 12 1 ASP N 23 ? ? -69.30 73.01 13 1 GLN H 15 ? ? -164.28 117.31 14 1 ALA H 21 ? ? -102.72 -60.30 15 1 GLU H 22 ? ? -103.31 -167.53 16 1 ASP H 23 ? ? -69.35 73.10 17 1 GLN O 15 ? ? -164.25 117.31 18 1 ALA O 21 ? ? -102.70 -60.32 19 1 GLU O 22 ? ? -103.31 -167.59 20 1 ASP O 23 ? ? -69.26 73.06 21 1 GLN I 15 ? ? -164.25 117.28 22 1 ALA I 21 ? ? -102.70 -60.26 23 1 GLU I 22 ? ? -103.38 -167.54 24 1 ASP I 23 ? ? -69.29 73.03 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9K0E _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 9K0E _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 2.8 _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 62839 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type HELICAL # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7.4 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type 'ORGANELLE OR CELLULAR COMPONENT' _em_entity_assembly.name 'Cryo-EM structure of Amyloid-beta42-4b polymorph 2' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1,2 # _em_imaging.entry_id 9K0E _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'TFS KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 1000 _em_imaging.nominal_defocus_max 2000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 9K0E _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9K0E _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _em_experiment.aggregation_state FILAMENT _em_experiment.entity_assembly_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 G ASP 1 ? A ASP 1 2 1 Y 1 G ALA 2 ? A ALA 2 3 1 Y 1 G GLU 3 ? A GLU 3 4 1 Y 1 G PHE 4 ? A PHE 4 5 1 Y 1 G ARG 5 ? A ARG 5 6 1 Y 1 G HIS 6 ? A HIS 6 7 1 Y 1 G ASP 7 ? A ASP 7 8 1 Y 1 G SER 8 ? A SER 8 9 1 Y 1 G GLY 9 ? A GLY 9 10 1 Y 1 G TYR 10 ? A TYR 10 11 1 Y 1 F GLY 9 ? B GLY 1 12 1 Y 1 F TYR 10 ? B TYR 2 13 1 Y 1 F PHE 20 ? B PHE 12 14 1 Y 1 F ALA 21 ? B ALA 13 15 1 Y 1 B ASP 1 ? C ASP 1 16 1 Y 1 B ALA 2 ? C ALA 2 17 1 Y 1 B GLU 3 ? C GLU 3 18 1 Y 1 B PHE 4 ? C PHE 4 19 1 Y 1 B ARG 5 ? C ARG 5 20 1 Y 1 B HIS 6 ? C HIS 6 21 1 Y 1 B ASP 7 ? C ASP 7 22 1 Y 1 B SER 8 ? C SER 8 23 1 Y 1 B GLY 9 ? C GLY 9 24 1 Y 1 B TYR 10 ? C TYR 10 25 1 Y 1 A GLY 9 ? D GLY 1 26 1 Y 1 A TYR 10 ? D TYR 2 27 1 Y 1 A PHE 20 ? D PHE 12 28 1 Y 1 A ALA 21 ? D ALA 13 29 1 Y 1 N ASP 1 ? E ASP 1 30 1 Y 1 N ALA 2 ? E ALA 2 31 1 Y 1 N GLU 3 ? E GLU 3 32 1 Y 1 N PHE 4 ? E PHE 4 33 1 Y 1 N ARG 5 ? E ARG 5 34 1 Y 1 N HIS 6 ? E HIS 6 35 1 Y 1 N ASP 7 ? E ASP 7 36 1 Y 1 N SER 8 ? E SER 8 37 1 Y 1 N GLY 9 ? E GLY 9 38 1 Y 1 N TYR 10 ? E TYR 10 39 1 Y 1 L GLY 9 ? F GLY 1 40 1 Y 1 L TYR 10 ? F TYR 2 41 1 Y 1 L PHE 20 ? F PHE 12 42 1 Y 1 L ALA 21 ? F ALA 13 43 1 Y 1 H ASP 1 ? G ASP 1 44 1 Y 1 H ALA 2 ? G ALA 2 45 1 Y 1 H GLU 3 ? G GLU 3 46 1 Y 1 H PHE 4 ? G PHE 4 47 1 Y 1 H ARG 5 ? G ARG 5 48 1 Y 1 H HIS 6 ? G HIS 6 49 1 Y 1 H ASP 7 ? G ASP 7 50 1 Y 1 H SER 8 ? G SER 8 51 1 Y 1 H GLY 9 ? G GLY 9 52 1 Y 1 H TYR 10 ? G TYR 10 53 1 Y 1 D GLY 9 ? H GLY 1 54 1 Y 1 D TYR 10 ? H TYR 2 55 1 Y 1 D PHE 20 ? H PHE 12 56 1 Y 1 D ALA 21 ? H ALA 13 57 1 Y 1 O ASP 1 ? I ASP 1 58 1 Y 1 O ALA 2 ? I ALA 2 59 1 Y 1 O GLU 3 ? I GLU 3 60 1 Y 1 O PHE 4 ? I PHE 4 61 1 Y 1 O ARG 5 ? I ARG 5 62 1 Y 1 O HIS 6 ? I HIS 6 63 1 Y 1 O ASP 7 ? I ASP 7 64 1 Y 1 O SER 8 ? I SER 8 65 1 Y 1 O GLY 9 ? I GLY 9 66 1 Y 1 O TYR 10 ? I TYR 10 67 1 Y 1 M GLY 9 ? J GLY 1 68 1 Y 1 M TYR 10 ? J TYR 2 69 1 Y 1 M PHE 20 ? J PHE 12 70 1 Y 1 M ALA 21 ? J ALA 13 71 1 Y 1 I ASP 1 ? K ASP 1 72 1 Y 1 I ALA 2 ? K ALA 2 73 1 Y 1 I GLU 3 ? K GLU 3 74 1 Y 1 I PHE 4 ? K PHE 4 75 1 Y 1 I ARG 5 ? K ARG 5 76 1 Y 1 I HIS 6 ? K HIS 6 77 1 Y 1 I ASP 7 ? K ASP 7 78 1 Y 1 I SER 8 ? K SER 8 79 1 Y 1 I GLY 9 ? K GLY 9 80 1 Y 1 I TYR 10 ? K TYR 10 81 1 Y 1 E GLY 9 ? L GLY 1 82 1 Y 1 E TYR 10 ? L TYR 2 83 1 Y 1 E PHE 20 ? L PHE 12 84 1 Y 1 E ALA 21 ? L ALA 13 # 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 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 GLN N N N N 74 GLN CA C N S 75 GLN C C N N 76 GLN O O N N 77 GLN CB C N N 78 GLN CG C N N 79 GLN CD C N N 80 GLN OE1 O N N 81 GLN NE2 N N N 82 GLN OXT O N N 83 GLN H H N N 84 GLN H2 H N N 85 GLN HA H N N 86 GLN HB2 H N N 87 GLN HB3 H N N 88 GLN HG2 H N N 89 GLN HG3 H N N 90 GLN HE21 H N N 91 GLN HE22 H N N 92 GLN HXT H N N 93 GLU N N N N 94 GLU CA C N S 95 GLU C C N N 96 GLU O O N N 97 GLU CB C N N 98 GLU CG C N N 99 GLU CD C N N 100 GLU OE1 O N N 101 GLU OE2 O N N 102 GLU OXT O N N 103 GLU H H N N 104 GLU H2 H N N 105 GLU HA H N N 106 GLU HB2 H N N 107 GLU HB3 H N N 108 GLU HG2 H N N 109 GLU HG3 H N N 110 GLU HE2 H N N 111 GLU HXT H N N 112 GLY N N N N 113 GLY CA C N N 114 GLY C C N N 115 GLY O O N N 116 GLY OXT O N N 117 GLY H H N N 118 GLY H2 H N N 119 GLY HA2 H N N 120 GLY HA3 H N N 121 GLY HXT H N N 122 HIS N N N N 123 HIS CA C N S 124 HIS C C N N 125 HIS O O N N 126 HIS CB C N N 127 HIS CG C Y N 128 HIS ND1 N Y N 129 HIS CD2 C Y N 130 HIS CE1 C Y N 131 HIS NE2 N Y N 132 HIS OXT O N N 133 HIS H H N N 134 HIS H2 H N N 135 HIS HA H N N 136 HIS HB2 H N N 137 HIS HB3 H N N 138 HIS HD1 H N N 139 HIS HD2 H N N 140 HIS HE1 H N N 141 HIS HE2 H N N 142 HIS HXT H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 ILE N N N N 147 ILE CA C N S 148 ILE C C N N 149 ILE O O N N 150 ILE CB C N S 151 ILE CG1 C N N 152 ILE CG2 C N N 153 ILE CD1 C N N 154 ILE OXT O N N 155 ILE H H N N 156 ILE H2 H N N 157 ILE HA H N N 158 ILE HB H N N 159 ILE HG12 H N N 160 ILE HG13 H N N 161 ILE HG21 H N N 162 ILE HG22 H N N 163 ILE HG23 H N N 164 ILE HD11 H N N 165 ILE HD12 H N N 166 ILE HD13 H N N 167 ILE HXT H N N 168 LEU N N N N 169 LEU CA C N S 170 LEU C C N N 171 LEU O O N N 172 LEU CB C N N 173 LEU CG C N N 174 LEU CD1 C N N 175 LEU CD2 C N N 176 LEU OXT O N N 177 LEU H H N N 178 LEU H2 H N N 179 LEU HA H N N 180 LEU HB2 H N N 181 LEU HB3 H N N 182 LEU HG H N N 183 LEU HD11 H N N 184 LEU HD12 H N N 185 LEU HD13 H N N 186 LEU HD21 H N N 187 LEU HD22 H N N 188 LEU HD23 H N N 189 LEU HXT H N N 190 LYS N N N N 191 LYS CA C N S 192 LYS C C N N 193 LYS O O N N 194 LYS CB C N N 195 LYS CG C N N 196 LYS CD C N N 197 LYS CE C N N 198 LYS NZ N N N 199 LYS OXT O N N 200 LYS H H N N 201 LYS H2 H N N 202 LYS HA H N N 203 LYS HB2 H N N 204 LYS HB3 H N N 205 LYS HG2 H N N 206 LYS HG3 H N N 207 LYS HD2 H N N 208 LYS HD3 H N N 209 LYS HE2 H N N 210 LYS HE3 H N N 211 LYS HZ1 H N N 212 LYS HZ2 H N N 213 LYS HZ3 H N N 214 LYS HXT H N N 215 MET N N N N 216 MET CA C N S 217 MET C C N N 218 MET O O N N 219 MET CB C N N 220 MET CG C N N 221 MET SD S N N 222 MET CE C N N 223 MET OXT O N N 224 MET H H N N 225 MET H2 H N N 226 MET HA H N N 227 MET HB2 H N N 228 MET HB3 H N N 229 MET HG2 H N N 230 MET HG3 H N N 231 MET HE1 H N N 232 MET HE2 H N N 233 MET HE3 H N N 234 MET HXT H N N 235 PHE N N N N 236 PHE CA C N S 237 PHE C C N N 238 PHE O O N N 239 PHE CB C N N 240 PHE CG C Y N 241 PHE CD1 C Y N 242 PHE CD2 C Y N 243 PHE CE1 C Y N 244 PHE CE2 C Y N 245 PHE CZ C Y N 246 PHE OXT O N N 247 PHE H H N N 248 PHE H2 H N N 249 PHE HA H N N 250 PHE HB2 H N N 251 PHE HB3 H N N 252 PHE HD1 H N N 253 PHE HD2 H N N 254 PHE HE1 H N N 255 PHE HE2 H N N 256 PHE HZ H N N 257 PHE HXT H N N 258 SER N N N N 259 SER CA C N S 260 SER C C N N 261 SER O O N N 262 SER CB C N N 263 SER OG O N N 264 SER OXT O N N 265 SER H H N N 266 SER H2 H N N 267 SER HA H N N 268 SER HB2 H N N 269 SER HB3 H N N 270 SER HG H N N 271 SER HXT H N N 272 TYR N N N N 273 TYR CA C N S 274 TYR C C N N 275 TYR O O N N 276 TYR CB C N N 277 TYR CG C Y N 278 TYR CD1 C Y N 279 TYR CD2 C Y N 280 TYR CE1 C Y N 281 TYR CE2 C Y N 282 TYR CZ C Y N 283 TYR OH O N N 284 TYR OXT O N N 285 TYR H H N N 286 TYR H2 H N N 287 TYR HA H N N 288 TYR HB2 H N N 289 TYR HB3 H N N 290 TYR HD1 H N N 291 TYR HD2 H N N 292 TYR HE1 H N N 293 TYR HE2 H N N 294 TYR HH H N N 295 TYR HXT H N N 296 VAL N N N N 297 VAL CA C N S 298 VAL C C N N 299 VAL O O N N 300 VAL CB C N N 301 VAL CG1 C N N 302 VAL CG2 C N N 303 VAL OXT O N N 304 VAL H H N N 305 VAL H2 H N N 306 VAL HA H N N 307 VAL HB H N N 308 VAL HG11 H N N 309 VAL HG12 H N N 310 VAL HG13 H N N 311 VAL HG21 H N N 312 VAL HG22 H N N 313 VAL HG23 H N N 314 VAL HXT H N N 315 # 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 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 GLN N CA sing N N 70 GLN N H sing N N 71 GLN N H2 sing N N 72 GLN CA C sing N N 73 GLN CA CB sing N N 74 GLN CA HA sing N N 75 GLN C O doub N N 76 GLN C OXT sing N N 77 GLN CB CG sing N N 78 GLN CB HB2 sing N N 79 GLN CB HB3 sing N N 80 GLN CG CD sing N N 81 GLN CG HG2 sing N N 82 GLN CG HG3 sing N N 83 GLN CD OE1 doub N N 84 GLN CD NE2 sing N N 85 GLN NE2 HE21 sing N N 86 GLN NE2 HE22 sing N N 87 GLN OXT HXT sing N N 88 GLU N CA sing N N 89 GLU N H sing N N 90 GLU N H2 sing N N 91 GLU CA C sing N N 92 GLU CA CB sing N N 93 GLU CA HA sing N N 94 GLU C O doub N N 95 GLU C OXT sing N N 96 GLU CB CG sing N N 97 GLU CB HB2 sing N N 98 GLU CB HB3 sing N N 99 GLU CG CD sing N N 100 GLU CG HG2 sing N N 101 GLU CG HG3 sing N N 102 GLU CD OE1 doub N N 103 GLU CD OE2 sing N N 104 GLU OE2 HE2 sing N N 105 GLU OXT HXT sing N N 106 GLY N CA sing N N 107 GLY N H sing N N 108 GLY N H2 sing N N 109 GLY CA C sing N N 110 GLY CA HA2 sing N N 111 GLY CA HA3 sing N N 112 GLY C O doub N N 113 GLY C OXT sing N N 114 GLY OXT HXT sing N N 115 HIS N CA sing N N 116 HIS N H sing N N 117 HIS N H2 sing N N 118 HIS CA C sing N N 119 HIS CA CB sing N N 120 HIS CA HA sing N N 121 HIS C O doub N N 122 HIS C OXT sing N N 123 HIS CB CG sing N N 124 HIS CB HB2 sing N N 125 HIS CB HB3 sing N N 126 HIS CG ND1 sing Y N 127 HIS CG CD2 doub Y N 128 HIS ND1 CE1 doub Y N 129 HIS ND1 HD1 sing N N 130 HIS CD2 NE2 sing Y N 131 HIS CD2 HD2 sing N N 132 HIS CE1 NE2 sing Y N 133 HIS CE1 HE1 sing N N 134 HIS NE2 HE2 sing N N 135 HIS OXT HXT sing N N 136 HOH O H1 sing N N 137 HOH O H2 sing N N 138 ILE N CA sing N N 139 ILE N H sing N N 140 ILE N H2 sing N N 141 ILE CA C sing N N 142 ILE CA CB sing N N 143 ILE CA HA sing N N 144 ILE C O doub N N 145 ILE C OXT sing N N 146 ILE CB CG1 sing N N 147 ILE CB CG2 sing N N 148 ILE CB HB sing N N 149 ILE CG1 CD1 sing N N 150 ILE CG1 HG12 sing N N 151 ILE CG1 HG13 sing N N 152 ILE CG2 HG21 sing N N 153 ILE CG2 HG22 sing N N 154 ILE CG2 HG23 sing N N 155 ILE CD1 HD11 sing N N 156 ILE CD1 HD12 sing N N 157 ILE CD1 HD13 sing N N 158 ILE OXT HXT sing N N 159 LEU N CA sing N N 160 LEU N H sing N N 161 LEU N H2 sing N N 162 LEU CA C sing N N 163 LEU CA CB sing N N 164 LEU CA HA sing N N 165 LEU C O doub N N 166 LEU C OXT sing N N 167 LEU CB CG sing N N 168 LEU CB HB2 sing N N 169 LEU CB HB3 sing N N 170 LEU CG CD1 sing N N 171 LEU CG CD2 sing N N 172 LEU CG HG sing N N 173 LEU CD1 HD11 sing N N 174 LEU CD1 HD12 sing N N 175 LEU CD1 HD13 sing N N 176 LEU CD2 HD21 sing N N 177 LEU CD2 HD22 sing N N 178 LEU CD2 HD23 sing N N 179 LEU OXT HXT sing N N 180 LYS N CA sing N N 181 LYS N H sing N N 182 LYS N H2 sing N N 183 LYS CA C sing N N 184 LYS CA CB sing N N 185 LYS CA HA sing N N 186 LYS C O doub N N 187 LYS C OXT sing N N 188 LYS CB CG sing N N 189 LYS CB HB2 sing N N 190 LYS CB HB3 sing N N 191 LYS CG CD sing N N 192 LYS CG HG2 sing N N 193 LYS CG HG3 sing N N 194 LYS CD CE sing N N 195 LYS CD HD2 sing N N 196 LYS CD HD3 sing N N 197 LYS CE NZ sing N N 198 LYS CE HE2 sing N N 199 LYS CE HE3 sing N N 200 LYS NZ HZ1 sing N N 201 LYS NZ HZ2 sing N N 202 LYS NZ HZ3 sing N N 203 LYS OXT HXT sing N N 204 MET N CA sing N N 205 MET N H sing N N 206 MET N H2 sing N N 207 MET CA C sing N N 208 MET CA CB sing N N 209 MET CA HA sing N N 210 MET C O doub N N 211 MET C OXT sing N N 212 MET CB CG sing N N 213 MET CB HB2 sing N N 214 MET CB HB3 sing N N 215 MET CG SD sing N N 216 MET CG HG2 sing N N 217 MET CG HG3 sing N N 218 MET SD CE sing N N 219 MET CE HE1 sing N N 220 MET CE HE2 sing N N 221 MET CE HE3 sing N N 222 MET OXT HXT sing N N 223 PHE N CA sing N N 224 PHE N H sing N N 225 PHE N H2 sing N N 226 PHE CA C sing N N 227 PHE CA CB sing N N 228 PHE CA HA sing N N 229 PHE C O doub N N 230 PHE C OXT sing N N 231 PHE CB CG sing N N 232 PHE CB HB2 sing N N 233 PHE CB HB3 sing N N 234 PHE CG CD1 doub Y N 235 PHE CG CD2 sing Y N 236 PHE CD1 CE1 sing Y N 237 PHE CD1 HD1 sing N N 238 PHE CD2 CE2 doub Y N 239 PHE CD2 HD2 sing N N 240 PHE CE1 CZ doub Y N 241 PHE CE1 HE1 sing N N 242 PHE CE2 CZ sing Y N 243 PHE CE2 HE2 sing N N 244 PHE CZ HZ sing N N 245 PHE OXT HXT sing N N 246 SER N CA sing N N 247 SER N H sing N N 248 SER N H2 sing N N 249 SER CA C sing N N 250 SER CA CB sing N N 251 SER CA HA sing N N 252 SER C O doub N N 253 SER C OXT sing N N 254 SER CB OG sing N N 255 SER CB HB2 sing N N 256 SER CB HB3 sing N N 257 SER OG HG sing N N 258 SER OXT HXT sing N N 259 TYR N CA sing N N 260 TYR N H sing N N 261 TYR N H2 sing N N 262 TYR CA C sing N N 263 TYR CA CB sing N N 264 TYR CA HA sing N N 265 TYR C O doub N N 266 TYR C OXT sing N N 267 TYR CB CG sing N N 268 TYR CB HB2 sing N N 269 TYR CB HB3 sing N N 270 TYR CG CD1 doub Y N 271 TYR CG CD2 sing Y N 272 TYR CD1 CE1 sing Y N 273 TYR CD1 HD1 sing N N 274 TYR CD2 CE2 doub Y N 275 TYR CD2 HD2 sing N N 276 TYR CE1 CZ doub Y N 277 TYR CE1 HE1 sing N N 278 TYR CE2 CZ sing Y N 279 TYR CE2 HE2 sing N N 280 TYR CZ OH sing N N 281 TYR OH HH sing N N 282 TYR OXT HXT sing N N 283 VAL N CA sing N N 284 VAL N H sing N N 285 VAL N H2 sing N N 286 VAL CA C sing N N 287 VAL CA CB sing N N 288 VAL CA HA sing N N 289 VAL C O doub N N 290 VAL C OXT sing N N 291 VAL CB CG1 sing N N 292 VAL CB CG2 sing N N 293 VAL CB HB sing N N 294 VAL CG1 HG11 sing N N 295 VAL CG1 HG12 sing N N 296 VAL CG1 HG13 sing N N 297 VAL CG2 HG21 sing N N 298 VAL CG2 HG22 sing N N 299 VAL CG2 HG23 sing N N 300 VAL OXT HXT sing N N 301 # _em_admin.current_status REL _em_admin.deposition_date 2024-10-15 _em_admin.deposition_site PDBJ _em_admin.entry_id 9K0E _em_admin.last_update 2025-08-06 _em_admin.map_release_date 2025-08-06 _em_admin.title 'Cryo-EM structure of Amyloid-beta42-4b polymorph 2' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type NONE # _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 9606 _em_entity_assembly_naturalsource.organism 'Homo sapiens' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.details ? _em_helical_entity.axial_symmetry C1 _em_helical_entity.angular_rotation_per_subunit 179.66 _em_helical_entity.axial_rise_per_subunit 2.42 # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 55 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 BIOCONTINUUM (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'MODEL REFINEMENT' ? 2 ? ? ? PHENIX 1.15.2_3472: 'IMAGE ACQUISITION' ? 3 ? ? 1 ? ? MASKING ? 4 ? ? ? ? ? 'CTF CORRECTION' ? 5 1 ? ? ? ? 'LAYERLINE INDEXING' ? 6 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 7 ? ? ? ? ? 'MODEL FITTING' ? 8 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? 'VOLUME SELECTION' ? 14 1 1 1 ? ? 'SERIES ALIGNMENT' ? 15 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 16 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 17 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 18 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 19 1 1 1 ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Not funded' _pdbx_audit_support.country ? _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 9K0E _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_ #