data_8Z93 # _entry.id 8Z93 # _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 8Z93 pdb_00008z93 10.2210/pdb8z93/pdb WWPDB D_1300047229 ? ? EMDB EMD-39853 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-04-30 ? 2 'EM metadata' 1 0 2025-04-30 ? 3 FSC 1 0 2025-04-30 ? 4 'Half map' 1 0 2025-04-30 1 5 'Half map' 1 0 2025-04-30 2 6 Image 1 0 2025-04-30 ? 7 'Primary map' 1 0 2025-04-30 ? 8 'Structure model' 1 1 2025-07-16 ? 9 'EM metadata' 1 1 2025-07-16 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? 3 3 FSC repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 'Half map' repository 'Initial release' ? ? 6 6 Image repository 'Initial release' ? ? 7 7 'Primary map' repository 'Initial release' ? ? # 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 8 'Structure model' 'Data collection' 2 9 'EM metadata' 'Data processing' 3 9 'EM metadata' 'Experimental summary' # 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 8 'Structure model' em_admin 2 8 'Structure model' em_software 3 9 'EM metadata' em_admin 4 9 'EM metadata' em_software # 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 8 'Structure model' '_em_admin.last_update' 2 8 'Structure model' '_em_software.name' 3 9 'EM metadata' '_em_admin.last_update' 4 9 'EM metadata' '_em_software.name' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8Z93 _pdbx_database_status.recvd_initial_deposition_date 2024-04-22 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBC _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 fibril formed by human RIPK1 RHIM protein' _pdbx_database_related.db_id EMD-39853 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email liulab@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 'Ma, Y.' 1 ? 'Zhao, K.' 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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Cryo-EM structure of amyloid fibril formed by human RIPK1 RHIM protein' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ma, Y.' 1 ? primary 'Zhao, K.' 2 ? primary 'Liu, C.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Receptor-interacting serine/threonine-protein kinase 1' _entity.formula_weight 10916.004 _entity.pdbx_number_of_molecules 3 _entity.pdbx_ec 2.7.11.1 _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Cell death protein RIP,Receptor-interacting protein 1,RIP-1' # _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 ;MGHMPSLHNIPVPETNYLGNTPTMPFSSLPPTDESIKYTIYNSTGIQIGAYNYMEIGGTSSSLLDSTNTNFKEEPAAKYQ AIFDNTTSLTLEHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;MGHMPSLHNIPVPETNYLGNTPTMPFSSLPPTDESIKYTIYNSTGIQIGAYNYMEIGGTSSSLLDSTNTNFKEEPAAKYQ AIFDNTTSLTLEHHHHHH ; _entity_poly.pdbx_strand_id A,B,C _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 GLY n 1 3 HIS n 1 4 MET n 1 5 PRO n 1 6 SER n 1 7 LEU n 1 8 HIS n 1 9 ASN n 1 10 ILE n 1 11 PRO n 1 12 VAL n 1 13 PRO n 1 14 GLU n 1 15 THR n 1 16 ASN n 1 17 TYR n 1 18 LEU n 1 19 GLY n 1 20 ASN n 1 21 THR n 1 22 PRO n 1 23 THR n 1 24 MET n 1 25 PRO n 1 26 PHE n 1 27 SER n 1 28 SER n 1 29 LEU n 1 30 PRO n 1 31 PRO n 1 32 THR n 1 33 ASP n 1 34 GLU n 1 35 SER n 1 36 ILE n 1 37 LYS n 1 38 TYR n 1 39 THR n 1 40 ILE n 1 41 TYR n 1 42 ASN n 1 43 SER n 1 44 THR n 1 45 GLY n 1 46 ILE n 1 47 GLN n 1 48 ILE n 1 49 GLY n 1 50 ALA n 1 51 TYR n 1 52 ASN n 1 53 TYR n 1 54 MET n 1 55 GLU n 1 56 ILE n 1 57 GLY n 1 58 GLY n 1 59 THR n 1 60 SER n 1 61 SER n 1 62 SER n 1 63 LEU n 1 64 LEU n 1 65 ASP n 1 66 SER n 1 67 THR n 1 68 ASN n 1 69 THR n 1 70 ASN n 1 71 PHE n 1 72 LYS n 1 73 GLU n 1 74 GLU n 1 75 PRO n 1 76 ALA n 1 77 ALA n 1 78 LYS n 1 79 TYR n 1 80 GLN n 1 81 ALA n 1 82 ILE n 1 83 PHE n 1 84 ASP n 1 85 ASN n 1 86 THR n 1 87 THR n 1 88 SER n 1 89 LEU n 1 90 THR n 1 91 LEU n 1 92 GLU n 1 93 HIS n 1 94 HIS n 1 95 HIS n 1 96 HIS n 1 97 HIS n 1 98 HIS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 98 _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'RIPK1, RIP, RIP1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 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 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 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 MET 1 494 ? ? ? A . n A 1 2 GLY 2 495 ? ? ? A . n A 1 3 HIS 3 496 ? ? ? A . n A 1 4 MET 4 497 ? ? ? A . n A 1 5 PRO 5 498 ? ? ? A . n A 1 6 SER 6 499 ? ? ? A . n A 1 7 LEU 7 500 ? ? ? A . n A 1 8 HIS 8 501 ? ? ? A . n A 1 9 ASN 9 502 ? ? ? A . n A 1 10 ILE 10 503 ? ? ? A . n A 1 11 PRO 11 504 ? ? ? A . n A 1 12 VAL 12 505 ? ? ? A . n A 1 13 PRO 13 506 ? ? ? A . n A 1 14 GLU 14 507 ? ? ? A . n A 1 15 THR 15 508 ? ? ? A . n A 1 16 ASN 16 509 ? ? ? A . n A 1 17 TYR 17 510 ? ? ? A . n A 1 18 LEU 18 511 ? ? ? A . n A 1 19 GLY 19 512 ? ? ? A . n A 1 20 ASN 20 513 ? ? ? A . n A 1 21 THR 21 514 ? ? ? A . n A 1 22 PRO 22 515 ? ? ? A . n A 1 23 THR 23 516 ? ? ? A . n A 1 24 MET 24 517 ? ? ? A . n A 1 25 PRO 25 518 ? ? ? A . n A 1 26 PHE 26 519 ? ? ? A . n A 1 27 SER 27 520 ? ? ? A . n A 1 28 SER 28 521 ? ? ? A . n A 1 29 LEU 29 522 ? ? ? A . n A 1 30 PRO 30 523 ? ? ? A . n A 1 31 PRO 31 524 ? ? ? A . n A 1 32 THR 32 525 ? ? ? A . n A 1 33 ASP 33 526 ? ? ? A . n A 1 34 GLU 34 527 ? ? ? A . n A 1 35 SER 35 528 ? ? ? A . n A 1 36 ILE 36 529 ? ? ? A . n A 1 37 LYS 37 530 ? ? ? A . n A 1 38 TYR 38 531 531 TYR TYR A . n A 1 39 THR 39 532 532 THR THR A . n A 1 40 ILE 40 533 533 ILE ILE A . n A 1 41 TYR 41 534 534 TYR TYR A . n A 1 42 ASN 42 535 535 ASN ASN A . n A 1 43 SER 43 536 536 SER SER A . n A 1 44 THR 44 537 537 THR THR A . n A 1 45 GLY 45 538 538 GLY GLY A . n A 1 46 ILE 46 539 539 ILE ILE A . n A 1 47 GLN 47 540 540 GLN GLN A . n A 1 48 ILE 48 541 541 ILE ILE A . n A 1 49 GLY 49 542 542 GLY GLY A . n A 1 50 ALA 50 543 543 ALA ALA A . n A 1 51 TYR 51 544 544 TYR TYR A . n A 1 52 ASN 52 545 545 ASN ASN A . n A 1 53 TYR 53 546 546 TYR TYR A . n A 1 54 MET 54 547 547 MET MET A . n A 1 55 GLU 55 548 548 GLU GLU A . n A 1 56 ILE 56 549 549 ILE ILE A . n A 1 57 GLY 57 550 550 GLY GLY A . n A 1 58 GLY 58 551 ? ? ? A . n A 1 59 THR 59 552 ? ? ? A . n A 1 60 SER 60 553 ? ? ? A . n A 1 61 SER 61 554 ? ? ? A . n A 1 62 SER 62 555 ? ? ? A . n A 1 63 LEU 63 556 ? ? ? A . n A 1 64 LEU 64 557 ? ? ? A . n A 1 65 ASP 65 558 ? ? ? A . n A 1 66 SER 66 559 ? ? ? A . n A 1 67 THR 67 560 ? ? ? A . n A 1 68 ASN 68 561 ? ? ? A . n A 1 69 THR 69 562 ? ? ? A . n A 1 70 ASN 70 563 ? ? ? A . n A 1 71 PHE 71 564 ? ? ? A . n A 1 72 LYS 72 565 ? ? ? A . n A 1 73 GLU 73 566 ? ? ? A . n A 1 74 GLU 74 567 ? ? ? A . n A 1 75 PRO 75 568 ? ? ? A . n A 1 76 ALA 76 569 ? ? ? A . n A 1 77 ALA 77 570 ? ? ? A . n A 1 78 LYS 78 571 ? ? ? A . n A 1 79 TYR 79 572 ? ? ? A . n A 1 80 GLN 80 573 ? ? ? A . n A 1 81 ALA 81 574 ? ? ? A . n A 1 82 ILE 82 575 ? ? ? A . n A 1 83 PHE 83 576 ? ? ? A . n A 1 84 ASP 84 577 ? ? ? A . n A 1 85 ASN 85 578 ? ? ? A . n A 1 86 THR 86 579 ? ? ? A . n A 1 87 THR 87 580 ? ? ? A . n A 1 88 SER 88 581 ? ? ? A . n A 1 89 LEU 89 582 ? ? ? A . n A 1 90 THR 90 583 ? ? ? A . n A 1 91 LEU 91 584 ? ? ? A . n A 1 92 GLU 92 585 ? ? ? A . n A 1 93 HIS 93 586 ? ? ? A . n A 1 94 HIS 94 587 ? ? ? A . n A 1 95 HIS 95 588 ? ? ? A . n A 1 96 HIS 96 589 ? ? ? A . n A 1 97 HIS 97 590 ? ? ? A . n A 1 98 HIS 98 591 ? ? ? A . n B 1 1 MET 1 494 ? ? ? B . n B 1 2 GLY 2 495 ? ? ? B . n B 1 3 HIS 3 496 ? ? ? B . n B 1 4 MET 4 497 ? ? ? B . n B 1 5 PRO 5 498 ? ? ? B . n B 1 6 SER 6 499 ? ? ? B . n B 1 7 LEU 7 500 ? ? ? B . n B 1 8 HIS 8 501 ? ? ? B . n B 1 9 ASN 9 502 ? ? ? B . n B 1 10 ILE 10 503 ? ? ? B . n B 1 11 PRO 11 504 ? ? ? B . n B 1 12 VAL 12 505 ? ? ? B . n B 1 13 PRO 13 506 ? ? ? B . n B 1 14 GLU 14 507 ? ? ? B . n B 1 15 THR 15 508 ? ? ? B . n B 1 16 ASN 16 509 ? ? ? B . n B 1 17 TYR 17 510 ? ? ? B . n B 1 18 LEU 18 511 ? ? ? B . n B 1 19 GLY 19 512 ? ? ? B . n B 1 20 ASN 20 513 ? ? ? B . n B 1 21 THR 21 514 ? ? ? B . n B 1 22 PRO 22 515 ? ? ? B . n B 1 23 THR 23 516 ? ? ? B . n B 1 24 MET 24 517 ? ? ? B . n B 1 25 PRO 25 518 ? ? ? B . n B 1 26 PHE 26 519 ? ? ? B . n B 1 27 SER 27 520 ? ? ? B . n B 1 28 SER 28 521 ? ? ? B . n B 1 29 LEU 29 522 ? ? ? B . n B 1 30 PRO 30 523 ? ? ? B . n B 1 31 PRO 31 524 ? ? ? B . n B 1 32 THR 32 525 ? ? ? B . n B 1 33 ASP 33 526 ? ? ? B . n B 1 34 GLU 34 527 ? ? ? B . n B 1 35 SER 35 528 ? ? ? B . n B 1 36 ILE 36 529 ? ? ? B . n B 1 37 LYS 37 530 ? ? ? B . n B 1 38 TYR 38 531 531 TYR TYR B . n B 1 39 THR 39 532 532 THR THR B . n B 1 40 ILE 40 533 533 ILE ILE B . n B 1 41 TYR 41 534 534 TYR TYR B . n B 1 42 ASN 42 535 535 ASN ASN B . n B 1 43 SER 43 536 536 SER SER B . n B 1 44 THR 44 537 537 THR THR B . n B 1 45 GLY 45 538 538 GLY GLY B . n B 1 46 ILE 46 539 539 ILE ILE B . n B 1 47 GLN 47 540 540 GLN GLN B . n B 1 48 ILE 48 541 541 ILE ILE B . n B 1 49 GLY 49 542 542 GLY GLY B . n B 1 50 ALA 50 543 543 ALA ALA B . n B 1 51 TYR 51 544 544 TYR TYR B . n B 1 52 ASN 52 545 545 ASN ASN B . n B 1 53 TYR 53 546 546 TYR TYR B . n B 1 54 MET 54 547 547 MET MET B . n B 1 55 GLU 55 548 548 GLU GLU B . n B 1 56 ILE 56 549 549 ILE ILE B . n B 1 57 GLY 57 550 550 GLY GLY B . n B 1 58 GLY 58 551 ? ? ? B . n B 1 59 THR 59 552 ? ? ? B . n B 1 60 SER 60 553 ? ? ? B . n B 1 61 SER 61 554 ? ? ? B . n B 1 62 SER 62 555 ? ? ? B . n B 1 63 LEU 63 556 ? ? ? B . n B 1 64 LEU 64 557 ? ? ? B . n B 1 65 ASP 65 558 ? ? ? B . n B 1 66 SER 66 559 ? ? ? B . n B 1 67 THR 67 560 ? ? ? B . n B 1 68 ASN 68 561 ? ? ? B . n B 1 69 THR 69 562 ? ? ? B . n B 1 70 ASN 70 563 ? ? ? B . n B 1 71 PHE 71 564 ? ? ? B . n B 1 72 LYS 72 565 ? ? ? B . n B 1 73 GLU 73 566 ? ? ? B . n B 1 74 GLU 74 567 ? ? ? B . n B 1 75 PRO 75 568 ? ? ? B . n B 1 76 ALA 76 569 ? ? ? B . n B 1 77 ALA 77 570 ? ? ? B . n B 1 78 LYS 78 571 ? ? ? B . n B 1 79 TYR 79 572 ? ? ? B . n B 1 80 GLN 80 573 ? ? ? B . n B 1 81 ALA 81 574 ? ? ? B . n B 1 82 ILE 82 575 ? ? ? B . n B 1 83 PHE 83 576 ? ? ? B . n B 1 84 ASP 84 577 ? ? ? B . n B 1 85 ASN 85 578 ? ? ? B . n B 1 86 THR 86 579 ? ? ? B . n B 1 87 THR 87 580 ? ? ? B . n B 1 88 SER 88 581 ? ? ? B . n B 1 89 LEU 89 582 ? ? ? B . n B 1 90 THR 90 583 ? ? ? B . n B 1 91 LEU 91 584 ? ? ? B . n B 1 92 GLU 92 585 ? ? ? B . n B 1 93 HIS 93 586 ? ? ? B . n B 1 94 HIS 94 587 ? ? ? B . n B 1 95 HIS 95 588 ? ? ? B . n B 1 96 HIS 96 589 ? ? ? B . n B 1 97 HIS 97 590 ? ? ? B . n B 1 98 HIS 98 591 ? ? ? B . n C 1 1 MET 1 494 ? ? ? C . n C 1 2 GLY 2 495 ? ? ? C . n C 1 3 HIS 3 496 ? ? ? C . n C 1 4 MET 4 497 ? ? ? C . n C 1 5 PRO 5 498 ? ? ? C . n C 1 6 SER 6 499 ? ? ? C . n C 1 7 LEU 7 500 ? ? ? C . n C 1 8 HIS 8 501 ? ? ? C . n C 1 9 ASN 9 502 ? ? ? C . n C 1 10 ILE 10 503 ? ? ? C . n C 1 11 PRO 11 504 ? ? ? C . n C 1 12 VAL 12 505 ? ? ? C . n C 1 13 PRO 13 506 ? ? ? C . n C 1 14 GLU 14 507 ? ? ? C . n C 1 15 THR 15 508 ? ? ? C . n C 1 16 ASN 16 509 ? ? ? C . n C 1 17 TYR 17 510 ? ? ? C . n C 1 18 LEU 18 511 ? ? ? C . n C 1 19 GLY 19 512 ? ? ? C . n C 1 20 ASN 20 513 ? ? ? C . n C 1 21 THR 21 514 ? ? ? C . n C 1 22 PRO 22 515 ? ? ? C . n C 1 23 THR 23 516 ? ? ? C . n C 1 24 MET 24 517 ? ? ? C . n C 1 25 PRO 25 518 ? ? ? C . n C 1 26 PHE 26 519 ? ? ? C . n C 1 27 SER 27 520 ? ? ? C . n C 1 28 SER 28 521 ? ? ? C . n C 1 29 LEU 29 522 ? ? ? C . n C 1 30 PRO 30 523 ? ? ? C . n C 1 31 PRO 31 524 ? ? ? C . n C 1 32 THR 32 525 ? ? ? C . n C 1 33 ASP 33 526 ? ? ? C . n C 1 34 GLU 34 527 ? ? ? C . n C 1 35 SER 35 528 ? ? ? C . n C 1 36 ILE 36 529 ? ? ? C . n C 1 37 LYS 37 530 ? ? ? C . n C 1 38 TYR 38 531 531 TYR TYR C . n C 1 39 THR 39 532 532 THR THR C . n C 1 40 ILE 40 533 533 ILE ILE C . n C 1 41 TYR 41 534 534 TYR TYR C . n C 1 42 ASN 42 535 535 ASN ASN C . n C 1 43 SER 43 536 536 SER SER C . n C 1 44 THR 44 537 537 THR THR C . n C 1 45 GLY 45 538 538 GLY GLY C . n C 1 46 ILE 46 539 539 ILE ILE C . n C 1 47 GLN 47 540 540 GLN GLN C . n C 1 48 ILE 48 541 541 ILE ILE C . n C 1 49 GLY 49 542 542 GLY GLY C . n C 1 50 ALA 50 543 543 ALA ALA C . n C 1 51 TYR 51 544 544 TYR TYR C . n C 1 52 ASN 52 545 545 ASN ASN C . n C 1 53 TYR 53 546 546 TYR TYR C . n C 1 54 MET 54 547 547 MET MET C . n C 1 55 GLU 55 548 548 GLU GLU C . n C 1 56 ILE 56 549 549 ILE ILE C . n C 1 57 GLY 57 550 550 GLY GLY C . n C 1 58 GLY 58 551 ? ? ? C . n C 1 59 THR 59 552 ? ? ? C . n C 1 60 SER 60 553 ? ? ? C . n C 1 61 SER 61 554 ? ? ? C . n C 1 62 SER 62 555 ? ? ? C . n C 1 63 LEU 63 556 ? ? ? C . n C 1 64 LEU 64 557 ? ? ? C . n C 1 65 ASP 65 558 ? ? ? C . n C 1 66 SER 66 559 ? ? ? C . n C 1 67 THR 67 560 ? ? ? C . n C 1 68 ASN 68 561 ? ? ? C . n C 1 69 THR 69 562 ? ? ? C . n C 1 70 ASN 70 563 ? ? ? C . n C 1 71 PHE 71 564 ? ? ? C . n C 1 72 LYS 72 565 ? ? ? C . n C 1 73 GLU 73 566 ? ? ? C . n C 1 74 GLU 74 567 ? ? ? C . n C 1 75 PRO 75 568 ? ? ? C . n C 1 76 ALA 76 569 ? ? ? C . n C 1 77 ALA 77 570 ? ? ? C . n C 1 78 LYS 78 571 ? ? ? C . n C 1 79 TYR 79 572 ? ? ? C . n C 1 80 GLN 80 573 ? ? ? C . n C 1 81 ALA 81 574 ? ? ? C . n C 1 82 ILE 82 575 ? ? ? C . n C 1 83 PHE 83 576 ? ? ? C . n C 1 84 ASP 84 577 ? ? ? C . n C 1 85 ASN 85 578 ? ? ? C . n C 1 86 THR 86 579 ? ? ? C . n C 1 87 THR 87 580 ? ? ? C . n C 1 88 SER 88 581 ? ? ? C . n C 1 89 LEU 89 582 ? ? ? C . n C 1 90 THR 90 583 ? ? ? C . n C 1 91 LEU 91 584 ? ? ? C . n C 1 92 GLU 92 585 ? ? ? C . n C 1 93 HIS 93 586 ? ? ? C . n C 1 94 HIS 94 587 ? ? ? C . n C 1 95 HIS 95 588 ? ? ? C . n C 1 96 HIS 96 589 ? ? ? C . n C 1 97 HIS 97 590 ? ? ? C . n C 1 98 HIS 98 591 ? ? ? C . n # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8Z93 _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 8Z93 _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 8Z93 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 8Z93 _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' ? 0.006 ? 486 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 1.035 ? 657 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 5.719 ? 267 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.065 ? 69 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.005 ? 81 ? f_plane_restr ? ? # _struct.entry_id 8Z93 _struct.title 'Cryo-EM structure of amyloid fibril formed by human RIPK1 RHIM protein' _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 8Z93 _struct_keywords.text 'amyolid fibril, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code RIPK1_HUMAN _struct_ref.pdbx_db_accession Q13546 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;HMPSLHNIPVPETNYLGNTPTMPFSSLPPTDESIKYTIYNSTGIQIGAYNYMEIGGTSSSLLDSTNTNFKEEPAAKYQAI FDNTTSLT ; _struct_ref.pdbx_align_begin 496 # 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 8Z93 A 3 ? 90 ? Q13546 496 ? 583 ? 496 583 2 1 8Z93 B 3 ? 90 ? Q13546 496 ? 583 ? 496 583 3 1 8Z93 C 3 ? 90 ? Q13546 496 ? 583 ? 496 583 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 8Z93 MET A 1 ? UNP Q13546 ? ? 'initiating methionine' 494 1 1 8Z93 GLY A 2 ? UNP Q13546 ? ? 'expression tag' 495 2 1 8Z93 LEU A 91 ? UNP Q13546 ? ? 'expression tag' 584 3 1 8Z93 GLU A 92 ? UNP Q13546 ? ? 'expression tag' 585 4 1 8Z93 HIS A 93 ? UNP Q13546 ? ? 'expression tag' 586 5 1 8Z93 HIS A 94 ? UNP Q13546 ? ? 'expression tag' 587 6 1 8Z93 HIS A 95 ? UNP Q13546 ? ? 'expression tag' 588 7 1 8Z93 HIS A 96 ? UNP Q13546 ? ? 'expression tag' 589 8 1 8Z93 HIS A 97 ? UNP Q13546 ? ? 'expression tag' 590 9 1 8Z93 HIS A 98 ? UNP Q13546 ? ? 'expression tag' 591 10 2 8Z93 MET B 1 ? UNP Q13546 ? ? 'initiating methionine' 494 11 2 8Z93 GLY B 2 ? UNP Q13546 ? ? 'expression tag' 495 12 2 8Z93 LEU B 91 ? UNP Q13546 ? ? 'expression tag' 584 13 2 8Z93 GLU B 92 ? UNP Q13546 ? ? 'expression tag' 585 14 2 8Z93 HIS B 93 ? UNP Q13546 ? ? 'expression tag' 586 15 2 8Z93 HIS B 94 ? UNP Q13546 ? ? 'expression tag' 587 16 2 8Z93 HIS B 95 ? UNP Q13546 ? ? 'expression tag' 588 17 2 8Z93 HIS B 96 ? UNP Q13546 ? ? 'expression tag' 589 18 2 8Z93 HIS B 97 ? UNP Q13546 ? ? 'expression tag' 590 19 2 8Z93 HIS B 98 ? UNP Q13546 ? ? 'expression tag' 591 20 3 8Z93 MET C 1 ? UNP Q13546 ? ? 'initiating methionine' 494 21 3 8Z93 GLY C 2 ? UNP Q13546 ? ? 'expression tag' 495 22 3 8Z93 LEU C 91 ? UNP Q13546 ? ? 'expression tag' 584 23 3 8Z93 GLU C 92 ? UNP Q13546 ? ? 'expression tag' 585 24 3 8Z93 HIS C 93 ? UNP Q13546 ? ? 'expression tag' 586 25 3 8Z93 HIS C 94 ? UNP Q13546 ? ? 'expression tag' 587 26 3 8Z93 HIS C 95 ? UNP Q13546 ? ? 'expression tag' 588 27 3 8Z93 HIS C 96 ? UNP Q13546 ? ? 'expression tag' 589 28 3 8Z93 HIS C 97 ? UNP Q13546 ? ? 'expression tag' 590 29 3 8Z93 HIS C 98 ? UNP Q13546 ? ? 'expression tag' 591 30 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_entry_details.entry_id 8Z93 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 TYR _pdbx_validate_close_contact.auth_seq_id_1 531 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OG1 _pdbx_validate_close_contact.auth_asym_id_2 C _pdbx_validate_close_contact.auth_comp_id_2 THR _pdbx_validate_close_contact.auth_seq_id_2 532 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.06 # 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 ILE A 533 ? ? -98.98 -67.22 2 1 TYR A 534 ? ? 35.68 55.21 3 1 ASN A 535 ? ? -78.47 -162.35 4 1 ALA A 543 ? ? -160.96 -168.07 5 1 TYR A 546 ? ? -68.12 -179.65 6 1 ILE B 533 ? ? -98.92 -67.27 7 1 TYR B 534 ? ? 35.69 55.20 8 1 ASN B 535 ? ? -78.48 -162.26 9 1 ALA B 543 ? ? -160.99 -168.01 10 1 TYR B 546 ? ? -68.14 -179.61 11 1 ILE C 533 ? ? -98.95 -67.28 12 1 TYR C 534 ? ? 35.71 55.20 13 1 ASN C 535 ? ? -78.41 -162.35 14 1 ALA C 543 ? ? -160.97 -168.03 15 1 TYR C 546 ? ? -68.16 -179.62 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 8Z93 _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 8Z93 _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 4.65 _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 67812 _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 4.0 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type 'ORGANELLE OR CELLULAR COMPONENT' _em_entity_assembly.name 'human RIPK1 RHIM amyoid fibril' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 8Z93 _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 1300 _em_imaging.nominal_defocus_max 2300 _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 8Z93 _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 8Z93 _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _em_experiment.aggregation_state 'HELICAL ARRAY' _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 A MET 494 ? A MET 1 2 1 Y 1 A GLY 495 ? A GLY 2 3 1 Y 1 A HIS 496 ? A HIS 3 4 1 Y 1 A MET 497 ? A MET 4 5 1 Y 1 A PRO 498 ? A PRO 5 6 1 Y 1 A SER 499 ? A SER 6 7 1 Y 1 A LEU 500 ? A LEU 7 8 1 Y 1 A HIS 501 ? A HIS 8 9 1 Y 1 A ASN 502 ? A ASN 9 10 1 Y 1 A ILE 503 ? A ILE 10 11 1 Y 1 A PRO 504 ? A PRO 11 12 1 Y 1 A VAL 505 ? A VAL 12 13 1 Y 1 A PRO 506 ? A PRO 13 14 1 Y 1 A GLU 507 ? A GLU 14 15 1 Y 1 A THR 508 ? A THR 15 16 1 Y 1 A ASN 509 ? A ASN 16 17 1 Y 1 A TYR 510 ? A TYR 17 18 1 Y 1 A LEU 511 ? A LEU 18 19 1 Y 1 A GLY 512 ? A GLY 19 20 1 Y 1 A ASN 513 ? A ASN 20 21 1 Y 1 A THR 514 ? A THR 21 22 1 Y 1 A PRO 515 ? A PRO 22 23 1 Y 1 A THR 516 ? A THR 23 24 1 Y 1 A MET 517 ? A MET 24 25 1 Y 1 A PRO 518 ? A PRO 25 26 1 Y 1 A PHE 519 ? A PHE 26 27 1 Y 1 A SER 520 ? A SER 27 28 1 Y 1 A SER 521 ? A SER 28 29 1 Y 1 A LEU 522 ? A LEU 29 30 1 Y 1 A PRO 523 ? A PRO 30 31 1 Y 1 A PRO 524 ? A PRO 31 32 1 Y 1 A THR 525 ? A THR 32 33 1 Y 1 A ASP 526 ? A ASP 33 34 1 Y 1 A GLU 527 ? A GLU 34 35 1 Y 1 A SER 528 ? A SER 35 36 1 Y 1 A ILE 529 ? A ILE 36 37 1 Y 1 A LYS 530 ? A LYS 37 38 1 Y 1 A GLY 551 ? A GLY 58 39 1 Y 1 A THR 552 ? A THR 59 40 1 Y 1 A SER 553 ? A SER 60 41 1 Y 1 A SER 554 ? A SER 61 42 1 Y 1 A SER 555 ? A SER 62 43 1 Y 1 A LEU 556 ? A LEU 63 44 1 Y 1 A LEU 557 ? A LEU 64 45 1 Y 1 A ASP 558 ? A ASP 65 46 1 Y 1 A SER 559 ? A SER 66 47 1 Y 1 A THR 560 ? A THR 67 48 1 Y 1 A ASN 561 ? A ASN 68 49 1 Y 1 A THR 562 ? A THR 69 50 1 Y 1 A ASN 563 ? A ASN 70 51 1 Y 1 A PHE 564 ? A PHE 71 52 1 Y 1 A LYS 565 ? A LYS 72 53 1 Y 1 A GLU 566 ? A GLU 73 54 1 Y 1 A GLU 567 ? A GLU 74 55 1 Y 1 A PRO 568 ? A PRO 75 56 1 Y 1 A ALA 569 ? A ALA 76 57 1 Y 1 A ALA 570 ? A ALA 77 58 1 Y 1 A LYS 571 ? A LYS 78 59 1 Y 1 A TYR 572 ? A TYR 79 60 1 Y 1 A GLN 573 ? A GLN 80 61 1 Y 1 A ALA 574 ? A ALA 81 62 1 Y 1 A ILE 575 ? A ILE 82 63 1 Y 1 A PHE 576 ? A PHE 83 64 1 Y 1 A ASP 577 ? A ASP 84 65 1 Y 1 A ASN 578 ? A ASN 85 66 1 Y 1 A THR 579 ? A THR 86 67 1 Y 1 A THR 580 ? A THR 87 68 1 Y 1 A SER 581 ? A SER 88 69 1 Y 1 A LEU 582 ? A LEU 89 70 1 Y 1 A THR 583 ? A THR 90 71 1 Y 1 A LEU 584 ? A LEU 91 72 1 Y 1 A GLU 585 ? A GLU 92 73 1 Y 1 A HIS 586 ? A HIS 93 74 1 Y 1 A HIS 587 ? A HIS 94 75 1 Y 1 A HIS 588 ? A HIS 95 76 1 Y 1 A HIS 589 ? A HIS 96 77 1 Y 1 A HIS 590 ? A HIS 97 78 1 Y 1 A HIS 591 ? A HIS 98 79 1 Y 1 B MET 494 ? B MET 1 80 1 Y 1 B GLY 495 ? B GLY 2 81 1 Y 1 B HIS 496 ? B HIS 3 82 1 Y 1 B MET 497 ? B MET 4 83 1 Y 1 B PRO 498 ? B PRO 5 84 1 Y 1 B SER 499 ? B SER 6 85 1 Y 1 B LEU 500 ? B LEU 7 86 1 Y 1 B HIS 501 ? B HIS 8 87 1 Y 1 B ASN 502 ? B ASN 9 88 1 Y 1 B ILE 503 ? B ILE 10 89 1 Y 1 B PRO 504 ? B PRO 11 90 1 Y 1 B VAL 505 ? B VAL 12 91 1 Y 1 B PRO 506 ? B PRO 13 92 1 Y 1 B GLU 507 ? B GLU 14 93 1 Y 1 B THR 508 ? B THR 15 94 1 Y 1 B ASN 509 ? B ASN 16 95 1 Y 1 B TYR 510 ? B TYR 17 96 1 Y 1 B LEU 511 ? B LEU 18 97 1 Y 1 B GLY 512 ? B GLY 19 98 1 Y 1 B ASN 513 ? B ASN 20 99 1 Y 1 B THR 514 ? B THR 21 100 1 Y 1 B PRO 515 ? B PRO 22 101 1 Y 1 B THR 516 ? B THR 23 102 1 Y 1 B MET 517 ? B MET 24 103 1 Y 1 B PRO 518 ? B PRO 25 104 1 Y 1 B PHE 519 ? B PHE 26 105 1 Y 1 B SER 520 ? B SER 27 106 1 Y 1 B SER 521 ? B SER 28 107 1 Y 1 B LEU 522 ? B LEU 29 108 1 Y 1 B PRO 523 ? B PRO 30 109 1 Y 1 B PRO 524 ? B PRO 31 110 1 Y 1 B THR 525 ? B THR 32 111 1 Y 1 B ASP 526 ? B ASP 33 112 1 Y 1 B GLU 527 ? B GLU 34 113 1 Y 1 B SER 528 ? B SER 35 114 1 Y 1 B ILE 529 ? B ILE 36 115 1 Y 1 B LYS 530 ? B LYS 37 116 1 Y 1 B GLY 551 ? B GLY 58 117 1 Y 1 B THR 552 ? B THR 59 118 1 Y 1 B SER 553 ? B SER 60 119 1 Y 1 B SER 554 ? B SER 61 120 1 Y 1 B SER 555 ? B SER 62 121 1 Y 1 B LEU 556 ? B LEU 63 122 1 Y 1 B LEU 557 ? B LEU 64 123 1 Y 1 B ASP 558 ? B ASP 65 124 1 Y 1 B SER 559 ? B SER 66 125 1 Y 1 B THR 560 ? B THR 67 126 1 Y 1 B ASN 561 ? B ASN 68 127 1 Y 1 B THR 562 ? B THR 69 128 1 Y 1 B ASN 563 ? B ASN 70 129 1 Y 1 B PHE 564 ? B PHE 71 130 1 Y 1 B LYS 565 ? B LYS 72 131 1 Y 1 B GLU 566 ? B GLU 73 132 1 Y 1 B GLU 567 ? B GLU 74 133 1 Y 1 B PRO 568 ? B PRO 75 134 1 Y 1 B ALA 569 ? B ALA 76 135 1 Y 1 B ALA 570 ? B ALA 77 136 1 Y 1 B LYS 571 ? B LYS 78 137 1 Y 1 B TYR 572 ? B TYR 79 138 1 Y 1 B GLN 573 ? B GLN 80 139 1 Y 1 B ALA 574 ? B ALA 81 140 1 Y 1 B ILE 575 ? B ILE 82 141 1 Y 1 B PHE 576 ? B PHE 83 142 1 Y 1 B ASP 577 ? B ASP 84 143 1 Y 1 B ASN 578 ? B ASN 85 144 1 Y 1 B THR 579 ? B THR 86 145 1 Y 1 B THR 580 ? B THR 87 146 1 Y 1 B SER 581 ? B SER 88 147 1 Y 1 B LEU 582 ? B LEU 89 148 1 Y 1 B THR 583 ? B THR 90 149 1 Y 1 B LEU 584 ? B LEU 91 150 1 Y 1 B GLU 585 ? B GLU 92 151 1 Y 1 B HIS 586 ? B HIS 93 152 1 Y 1 B HIS 587 ? B HIS 94 153 1 Y 1 B HIS 588 ? B HIS 95 154 1 Y 1 B HIS 589 ? B HIS 96 155 1 Y 1 B HIS 590 ? B HIS 97 156 1 Y 1 B HIS 591 ? B HIS 98 157 1 Y 1 C MET 494 ? C MET 1 158 1 Y 1 C GLY 495 ? C GLY 2 159 1 Y 1 C HIS 496 ? C HIS 3 160 1 Y 1 C MET 497 ? C MET 4 161 1 Y 1 C PRO 498 ? C PRO 5 162 1 Y 1 C SER 499 ? C SER 6 163 1 Y 1 C LEU 500 ? C LEU 7 164 1 Y 1 C HIS 501 ? C HIS 8 165 1 Y 1 C ASN 502 ? C ASN 9 166 1 Y 1 C ILE 503 ? C ILE 10 167 1 Y 1 C PRO 504 ? C PRO 11 168 1 Y 1 C VAL 505 ? C VAL 12 169 1 Y 1 C PRO 506 ? C PRO 13 170 1 Y 1 C GLU 507 ? C GLU 14 171 1 Y 1 C THR 508 ? C THR 15 172 1 Y 1 C ASN 509 ? C ASN 16 173 1 Y 1 C TYR 510 ? C TYR 17 174 1 Y 1 C LEU 511 ? C LEU 18 175 1 Y 1 C GLY 512 ? C GLY 19 176 1 Y 1 C ASN 513 ? C ASN 20 177 1 Y 1 C THR 514 ? C THR 21 178 1 Y 1 C PRO 515 ? C PRO 22 179 1 Y 1 C THR 516 ? C THR 23 180 1 Y 1 C MET 517 ? C MET 24 181 1 Y 1 C PRO 518 ? C PRO 25 182 1 Y 1 C PHE 519 ? C PHE 26 183 1 Y 1 C SER 520 ? C SER 27 184 1 Y 1 C SER 521 ? C SER 28 185 1 Y 1 C LEU 522 ? C LEU 29 186 1 Y 1 C PRO 523 ? C PRO 30 187 1 Y 1 C PRO 524 ? C PRO 31 188 1 Y 1 C THR 525 ? C THR 32 189 1 Y 1 C ASP 526 ? C ASP 33 190 1 Y 1 C GLU 527 ? C GLU 34 191 1 Y 1 C SER 528 ? C SER 35 192 1 Y 1 C ILE 529 ? C ILE 36 193 1 Y 1 C LYS 530 ? C LYS 37 194 1 Y 1 C GLY 551 ? C GLY 58 195 1 Y 1 C THR 552 ? C THR 59 196 1 Y 1 C SER 553 ? C SER 60 197 1 Y 1 C SER 554 ? C SER 61 198 1 Y 1 C SER 555 ? C SER 62 199 1 Y 1 C LEU 556 ? C LEU 63 200 1 Y 1 C LEU 557 ? C LEU 64 201 1 Y 1 C ASP 558 ? C ASP 65 202 1 Y 1 C SER 559 ? C SER 66 203 1 Y 1 C THR 560 ? C THR 67 204 1 Y 1 C ASN 561 ? C ASN 68 205 1 Y 1 C THR 562 ? C THR 69 206 1 Y 1 C ASN 563 ? C ASN 70 207 1 Y 1 C PHE 564 ? C PHE 71 208 1 Y 1 C LYS 565 ? C LYS 72 209 1 Y 1 C GLU 566 ? C GLU 73 210 1 Y 1 C GLU 567 ? C GLU 74 211 1 Y 1 C PRO 568 ? C PRO 75 212 1 Y 1 C ALA 569 ? C ALA 76 213 1 Y 1 C ALA 570 ? C ALA 77 214 1 Y 1 C LYS 571 ? C LYS 78 215 1 Y 1 C TYR 572 ? C TYR 79 216 1 Y 1 C GLN 573 ? C GLN 80 217 1 Y 1 C ALA 574 ? C ALA 81 218 1 Y 1 C ILE 575 ? C ILE 82 219 1 Y 1 C PHE 576 ? C PHE 83 220 1 Y 1 C ASP 577 ? C ASP 84 221 1 Y 1 C ASN 578 ? C ASN 85 222 1 Y 1 C THR 579 ? C THR 86 223 1 Y 1 C THR 580 ? C THR 87 224 1 Y 1 C SER 581 ? C SER 88 225 1 Y 1 C LEU 582 ? C LEU 89 226 1 Y 1 C THR 583 ? C THR 90 227 1 Y 1 C LEU 584 ? C LEU 91 228 1 Y 1 C GLU 585 ? C GLU 92 229 1 Y 1 C HIS 586 ? C HIS 93 230 1 Y 1 C HIS 587 ? C HIS 94 231 1 Y 1 C HIS 588 ? C HIS 95 232 1 Y 1 C HIS 589 ? C HIS 96 233 1 Y 1 C HIS 590 ? C HIS 97 234 1 Y 1 C HIS 591 ? C HIS 98 # 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 ASN N N N N 14 ASN CA C N S 15 ASN C C N N 16 ASN O O N N 17 ASN CB C N N 18 ASN CG C N N 19 ASN OD1 O N N 20 ASN ND2 N N N 21 ASN OXT O N N 22 ASN H H N N 23 ASN H2 H N N 24 ASN HA H N N 25 ASN HB2 H N N 26 ASN HB3 H N N 27 ASN HD21 H N N 28 ASN HD22 H N N 29 ASN HXT H N N 30 ASP N N N N 31 ASP CA C N S 32 ASP C C N N 33 ASP O O N N 34 ASP CB C N N 35 ASP CG C N N 36 ASP OD1 O N N 37 ASP OD2 O N N 38 ASP OXT O N N 39 ASP H H N N 40 ASP H2 H N N 41 ASP HA H N N 42 ASP HB2 H N N 43 ASP HB3 H N N 44 ASP HD2 H N N 45 ASP HXT H N N 46 GLN N N N N 47 GLN CA C N S 48 GLN C C N N 49 GLN O O N N 50 GLN CB C N N 51 GLN CG C N N 52 GLN CD C N N 53 GLN OE1 O N N 54 GLN NE2 N N N 55 GLN OXT O N N 56 GLN H H N N 57 GLN H2 H N N 58 GLN HA H N N 59 GLN HB2 H N N 60 GLN HB3 H N N 61 GLN HG2 H N N 62 GLN HG3 H N N 63 GLN HE21 H N N 64 GLN HE22 H N N 65 GLN HXT H N N 66 GLU N N N N 67 GLU CA C N S 68 GLU C C N N 69 GLU O O N N 70 GLU CB C N N 71 GLU CG C N N 72 GLU CD C N N 73 GLU OE1 O N N 74 GLU OE2 O N N 75 GLU OXT O N N 76 GLU H H N N 77 GLU H2 H N N 78 GLU HA H N N 79 GLU HB2 H N N 80 GLU HB3 H N N 81 GLU HG2 H N N 82 GLU HG3 H N N 83 GLU HE2 H N N 84 GLU HXT H N N 85 GLY N N N N 86 GLY CA C N N 87 GLY C C N N 88 GLY O O N N 89 GLY OXT O N N 90 GLY H H N N 91 GLY H2 H N N 92 GLY HA2 H N N 93 GLY HA3 H N N 94 GLY HXT H N N 95 HIS N N N N 96 HIS CA C N S 97 HIS C C N N 98 HIS O O N N 99 HIS CB C N N 100 HIS CG C Y N 101 HIS ND1 N Y N 102 HIS CD2 C Y N 103 HIS CE1 C Y N 104 HIS NE2 N Y N 105 HIS OXT O N N 106 HIS H H N N 107 HIS H2 H N N 108 HIS HA H N N 109 HIS HB2 H N N 110 HIS HB3 H N N 111 HIS HD1 H N N 112 HIS HD2 H N N 113 HIS HE1 H N N 114 HIS HE2 H N N 115 HIS HXT H N N 116 ILE N N N N 117 ILE CA C N S 118 ILE C C N N 119 ILE O O N N 120 ILE CB C N S 121 ILE CG1 C N N 122 ILE CG2 C N N 123 ILE CD1 C N N 124 ILE OXT O N N 125 ILE H H N N 126 ILE H2 H N N 127 ILE HA H N N 128 ILE HB H N N 129 ILE HG12 H N N 130 ILE HG13 H N N 131 ILE HG21 H N N 132 ILE HG22 H N N 133 ILE HG23 H N N 134 ILE HD11 H N N 135 ILE HD12 H N N 136 ILE HD13 H N N 137 ILE HXT H N N 138 LEU N N N N 139 LEU CA C N S 140 LEU C C N N 141 LEU O O N N 142 LEU CB C N N 143 LEU CG C N N 144 LEU CD1 C N N 145 LEU CD2 C N N 146 LEU OXT O N N 147 LEU H H N N 148 LEU H2 H N N 149 LEU HA H N N 150 LEU HB2 H N N 151 LEU HB3 H N N 152 LEU HG H N N 153 LEU HD11 H N N 154 LEU HD12 H N N 155 LEU HD13 H N N 156 LEU HD21 H N N 157 LEU HD22 H N N 158 LEU HD23 H N N 159 LEU HXT H N N 160 LYS N N N N 161 LYS CA C N S 162 LYS C C N N 163 LYS O O N N 164 LYS CB C N N 165 LYS CG C N N 166 LYS CD C N N 167 LYS CE C N N 168 LYS NZ N N N 169 LYS OXT O N N 170 LYS H H N N 171 LYS H2 H N N 172 LYS HA H N N 173 LYS HB2 H N N 174 LYS HB3 H N N 175 LYS HG2 H N N 176 LYS HG3 H N N 177 LYS HD2 H N N 178 LYS HD3 H N N 179 LYS HE2 H N N 180 LYS HE3 H N N 181 LYS HZ1 H N N 182 LYS HZ2 H N N 183 LYS HZ3 H N N 184 LYS HXT H N N 185 MET N N N N 186 MET CA C N S 187 MET C C N N 188 MET O O N N 189 MET CB C N N 190 MET CG C N N 191 MET SD S N N 192 MET CE C N N 193 MET OXT O N N 194 MET H H N N 195 MET H2 H N N 196 MET HA H N N 197 MET HB2 H N N 198 MET HB3 H N N 199 MET HG2 H N N 200 MET HG3 H N N 201 MET HE1 H N N 202 MET HE2 H N N 203 MET HE3 H N N 204 MET HXT H N N 205 PHE N N N N 206 PHE CA C N S 207 PHE C C N N 208 PHE O O N N 209 PHE CB C N N 210 PHE CG C Y N 211 PHE CD1 C Y N 212 PHE CD2 C Y N 213 PHE CE1 C Y N 214 PHE CE2 C Y N 215 PHE CZ C Y N 216 PHE OXT O N N 217 PHE H H N N 218 PHE H2 H N N 219 PHE HA H N N 220 PHE HB2 H N N 221 PHE HB3 H N N 222 PHE HD1 H N N 223 PHE HD2 H N N 224 PHE HE1 H N N 225 PHE HE2 H N N 226 PHE HZ H N N 227 PHE HXT H N N 228 PRO N N N N 229 PRO CA C N S 230 PRO C C N N 231 PRO O O N N 232 PRO CB C N N 233 PRO CG C N N 234 PRO CD C N N 235 PRO OXT O N N 236 PRO H H N N 237 PRO HA H N N 238 PRO HB2 H N N 239 PRO HB3 H N N 240 PRO HG2 H N N 241 PRO HG3 H N N 242 PRO HD2 H N N 243 PRO HD3 H N N 244 PRO HXT H N N 245 SER N N N N 246 SER CA C N S 247 SER C C N N 248 SER O O N N 249 SER CB C N N 250 SER OG O N N 251 SER OXT O N N 252 SER H H N N 253 SER H2 H N N 254 SER HA H N N 255 SER HB2 H N N 256 SER HB3 H N N 257 SER HG H N N 258 SER HXT H N N 259 THR N N N N 260 THR CA C N S 261 THR C C N N 262 THR O O N N 263 THR CB C N R 264 THR OG1 O N N 265 THR CG2 C N N 266 THR OXT O N N 267 THR H H N N 268 THR H2 H N N 269 THR HA H N N 270 THR HB H N N 271 THR HG1 H N N 272 THR HG21 H N N 273 THR HG22 H N N 274 THR HG23 H N N 275 THR HXT H N N 276 TYR N N N N 277 TYR CA C N S 278 TYR C C N N 279 TYR O O N N 280 TYR CB C N N 281 TYR CG C Y N 282 TYR CD1 C Y N 283 TYR CD2 C Y N 284 TYR CE1 C Y N 285 TYR CE2 C Y N 286 TYR CZ C Y N 287 TYR OH O N N 288 TYR OXT O N N 289 TYR H H N N 290 TYR H2 H N N 291 TYR HA H N N 292 TYR HB2 H N N 293 TYR HB3 H N N 294 TYR HD1 H N N 295 TYR HD2 H N N 296 TYR HE1 H N N 297 TYR HE2 H N N 298 TYR HH H N N 299 TYR HXT H N N 300 VAL N N N N 301 VAL CA C N S 302 VAL C C N N 303 VAL O O N N 304 VAL CB C N N 305 VAL CG1 C N N 306 VAL CG2 C N N 307 VAL OXT O N N 308 VAL H H N N 309 VAL H2 H N N 310 VAL HA H N N 311 VAL HB H N N 312 VAL HG11 H N N 313 VAL HG12 H N N 314 VAL HG13 H N N 315 VAL HG21 H N N 316 VAL HG22 H N N 317 VAL HG23 H N N 318 VAL HXT H N N 319 # 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 ASN N CA sing N N 13 ASN N H sing N N 14 ASN N H2 sing N N 15 ASN CA C sing N N 16 ASN CA CB sing N N 17 ASN CA HA sing N N 18 ASN C O doub N N 19 ASN C OXT sing N N 20 ASN CB CG sing N N 21 ASN CB HB2 sing N N 22 ASN CB HB3 sing N N 23 ASN CG OD1 doub N N 24 ASN CG ND2 sing N N 25 ASN ND2 HD21 sing N N 26 ASN ND2 HD22 sing N N 27 ASN OXT HXT sing N N 28 ASP N CA sing N N 29 ASP N H sing N N 30 ASP N H2 sing N N 31 ASP CA C sing N N 32 ASP CA CB sing N N 33 ASP CA HA sing N N 34 ASP C O doub N N 35 ASP C OXT sing N N 36 ASP CB CG sing N N 37 ASP CB HB2 sing N N 38 ASP CB HB3 sing N N 39 ASP CG OD1 doub N N 40 ASP CG OD2 sing N N 41 ASP OD2 HD2 sing N N 42 ASP OXT HXT sing N N 43 GLN N CA sing N N 44 GLN N H sing N N 45 GLN N H2 sing N N 46 GLN CA C sing N N 47 GLN CA CB sing N N 48 GLN CA HA sing N N 49 GLN C O doub N N 50 GLN C OXT sing N N 51 GLN CB CG sing N N 52 GLN CB HB2 sing N N 53 GLN CB HB3 sing N N 54 GLN CG CD sing N N 55 GLN CG HG2 sing N N 56 GLN CG HG3 sing N N 57 GLN CD OE1 doub N N 58 GLN CD NE2 sing N N 59 GLN NE2 HE21 sing N N 60 GLN NE2 HE22 sing N N 61 GLN OXT HXT sing N N 62 GLU N CA sing N N 63 GLU N H sing N N 64 GLU N H2 sing N N 65 GLU CA C sing N N 66 GLU CA CB sing N N 67 GLU CA HA sing N N 68 GLU C O doub N N 69 GLU C OXT sing N N 70 GLU CB CG sing N N 71 GLU CB HB2 sing N N 72 GLU CB HB3 sing N N 73 GLU CG CD sing N N 74 GLU CG HG2 sing N N 75 GLU CG HG3 sing N N 76 GLU CD OE1 doub N N 77 GLU CD OE2 sing N N 78 GLU OE2 HE2 sing N N 79 GLU OXT HXT sing N N 80 GLY N CA sing N N 81 GLY N H sing N N 82 GLY N H2 sing N N 83 GLY CA C sing N N 84 GLY CA HA2 sing N N 85 GLY CA HA3 sing N N 86 GLY C O doub N N 87 GLY C OXT sing N N 88 GLY OXT HXT sing N N 89 HIS N CA sing N N 90 HIS N H sing N N 91 HIS N H2 sing N N 92 HIS CA C sing N N 93 HIS CA CB sing N N 94 HIS CA HA sing N N 95 HIS C O doub N N 96 HIS C OXT sing N N 97 HIS CB CG sing N N 98 HIS CB HB2 sing N N 99 HIS CB HB3 sing N N 100 HIS CG ND1 sing Y N 101 HIS CG CD2 doub Y N 102 HIS ND1 CE1 doub Y N 103 HIS ND1 HD1 sing N N 104 HIS CD2 NE2 sing Y N 105 HIS CD2 HD2 sing N N 106 HIS CE1 NE2 sing Y N 107 HIS CE1 HE1 sing N N 108 HIS NE2 HE2 sing N N 109 HIS OXT HXT sing N N 110 ILE N CA sing N N 111 ILE N H sing N N 112 ILE N H2 sing N N 113 ILE CA C sing N N 114 ILE CA CB sing N N 115 ILE CA HA sing N N 116 ILE C O doub N N 117 ILE C OXT sing N N 118 ILE CB CG1 sing N N 119 ILE CB CG2 sing N N 120 ILE CB HB sing N N 121 ILE CG1 CD1 sing N N 122 ILE CG1 HG12 sing N N 123 ILE CG1 HG13 sing N N 124 ILE CG2 HG21 sing N N 125 ILE CG2 HG22 sing N N 126 ILE CG2 HG23 sing N N 127 ILE CD1 HD11 sing N N 128 ILE CD1 HD12 sing N N 129 ILE CD1 HD13 sing N N 130 ILE OXT HXT sing N N 131 LEU N CA sing N N 132 LEU N H sing N N 133 LEU N H2 sing N N 134 LEU CA C sing N N 135 LEU CA CB sing N N 136 LEU CA HA sing N N 137 LEU C O doub N N 138 LEU C OXT sing N N 139 LEU CB CG sing N N 140 LEU CB HB2 sing N N 141 LEU CB HB3 sing N N 142 LEU CG CD1 sing N N 143 LEU CG CD2 sing N N 144 LEU CG HG sing N N 145 LEU CD1 HD11 sing N N 146 LEU CD1 HD12 sing N N 147 LEU CD1 HD13 sing N N 148 LEU CD2 HD21 sing N N 149 LEU CD2 HD22 sing N N 150 LEU CD2 HD23 sing N N 151 LEU OXT HXT sing N N 152 LYS N CA sing N N 153 LYS N H sing N N 154 LYS N H2 sing N N 155 LYS CA C sing N N 156 LYS CA CB sing N N 157 LYS CA HA sing N N 158 LYS C O doub N N 159 LYS C OXT sing N N 160 LYS CB CG sing N N 161 LYS CB HB2 sing N N 162 LYS CB HB3 sing N N 163 LYS CG CD sing N N 164 LYS CG HG2 sing N N 165 LYS CG HG3 sing N N 166 LYS CD CE sing N N 167 LYS CD HD2 sing N N 168 LYS CD HD3 sing N N 169 LYS CE NZ sing N N 170 LYS CE HE2 sing N N 171 LYS CE HE3 sing N N 172 LYS NZ HZ1 sing N N 173 LYS NZ HZ2 sing N N 174 LYS NZ HZ3 sing N N 175 LYS OXT HXT sing N N 176 MET N CA sing N N 177 MET N H sing N N 178 MET N H2 sing N N 179 MET CA C sing N N 180 MET CA CB sing N N 181 MET CA HA sing N N 182 MET C O doub N N 183 MET C OXT sing N N 184 MET CB CG sing N N 185 MET CB HB2 sing N N 186 MET CB HB3 sing N N 187 MET CG SD sing N N 188 MET CG HG2 sing N N 189 MET CG HG3 sing N N 190 MET SD CE sing N N 191 MET CE HE1 sing N N 192 MET CE HE2 sing N N 193 MET CE HE3 sing N N 194 MET OXT HXT sing N N 195 PHE N CA sing N N 196 PHE N H sing N N 197 PHE N H2 sing N N 198 PHE CA C sing N N 199 PHE CA CB sing N N 200 PHE CA HA sing N N 201 PHE C O doub N N 202 PHE C OXT sing N N 203 PHE CB CG sing N N 204 PHE CB HB2 sing N N 205 PHE CB HB3 sing N N 206 PHE CG CD1 doub Y N 207 PHE CG CD2 sing Y N 208 PHE CD1 CE1 sing Y N 209 PHE CD1 HD1 sing N N 210 PHE CD2 CE2 doub Y N 211 PHE CD2 HD2 sing N N 212 PHE CE1 CZ doub Y N 213 PHE CE1 HE1 sing N N 214 PHE CE2 CZ sing Y N 215 PHE CE2 HE2 sing N N 216 PHE CZ HZ sing N N 217 PHE OXT HXT sing N N 218 PRO N CA sing N N 219 PRO N CD sing N N 220 PRO N H sing N N 221 PRO CA C sing N N 222 PRO CA CB sing N N 223 PRO CA HA sing N N 224 PRO C O doub N N 225 PRO C OXT sing N N 226 PRO CB CG sing N N 227 PRO CB HB2 sing N N 228 PRO CB HB3 sing N N 229 PRO CG CD sing N N 230 PRO CG HG2 sing N N 231 PRO CG HG3 sing N N 232 PRO CD HD2 sing N N 233 PRO CD HD3 sing N N 234 PRO OXT HXT sing N N 235 SER N CA sing N N 236 SER N H sing N N 237 SER N H2 sing N N 238 SER CA C sing N N 239 SER CA CB sing N N 240 SER CA HA sing N N 241 SER C O doub N N 242 SER C OXT sing N N 243 SER CB OG sing N N 244 SER CB HB2 sing N N 245 SER CB HB3 sing N N 246 SER OG HG sing N N 247 SER OXT HXT sing N N 248 THR N CA sing N N 249 THR N H sing N N 250 THR N H2 sing N N 251 THR CA C sing N N 252 THR CA CB sing N N 253 THR CA HA sing N N 254 THR C O doub N N 255 THR C OXT sing N N 256 THR CB OG1 sing N N 257 THR CB CG2 sing N N 258 THR CB HB sing N N 259 THR OG1 HG1 sing N N 260 THR CG2 HG21 sing N N 261 THR CG2 HG22 sing N N 262 THR CG2 HG23 sing N N 263 THR OXT HXT sing N N 264 TYR N CA sing N N 265 TYR N H sing N N 266 TYR N H2 sing N N 267 TYR CA C sing N N 268 TYR CA CB sing N N 269 TYR CA HA sing N N 270 TYR C O doub N N 271 TYR C OXT sing N N 272 TYR CB CG sing N N 273 TYR CB HB2 sing N N 274 TYR CB HB3 sing N N 275 TYR CG CD1 doub Y N 276 TYR CG CD2 sing Y N 277 TYR CD1 CE1 sing Y N 278 TYR CD1 HD1 sing N N 279 TYR CD2 CE2 doub Y N 280 TYR CD2 HD2 sing N N 281 TYR CE1 CZ doub Y N 282 TYR CE1 HE1 sing N N 283 TYR CE2 CZ sing Y N 284 TYR CE2 HE2 sing N N 285 TYR CZ OH sing N N 286 TYR OH HH sing N N 287 TYR OXT HXT sing N N 288 VAL N CA sing N N 289 VAL N H sing N N 290 VAL N H2 sing N N 291 VAL CA C sing N N 292 VAL CA CB sing N N 293 VAL CA HA sing N N 294 VAL C O doub N N 295 VAL C OXT sing N N 296 VAL CB CG1 sing N N 297 VAL CB CG2 sing N N 298 VAL CB HB sing N N 299 VAL CG1 HG11 sing N N 300 VAL CG1 HG12 sing N N 301 VAL CG1 HG13 sing N N 302 VAL CG2 HG21 sing N N 303 VAL CG2 HG22 sing N N 304 VAL CG2 HG23 sing N N 305 VAL OXT HXT sing N N 306 # _em_admin.current_status REL _em_admin.deposition_date 2024-04-22 _em_admin.deposition_site PDBJ _em_admin.entry_id 8Z93 _em_admin.last_update 2025-07-16 _em_admin.map_release_date 2025-04-30 _em_admin.title 'Cryo-EM structure of amyloid fibril formed by human RIPK1 RHIM protein' # _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_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 562 _em_entity_assembly_recombinant.organism 'Escherichia coli' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.details ? _em_helical_entity.axial_symmetry C1 _em_helical_entity.angular_rotation_per_subunit -6.59 _em_helical_entity.axial_rise_per_subunit 4.84 # _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 BIOQUANTUM (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 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? ? ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? ? ? ? ? 'MODEL REFINEMENT' ? 8 ? ? ? PHENIX ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 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 'National Natural Science Foundation of China (NSFC)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number 82188101 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 8Z93 _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_ #