Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class with Sec62

2025-06-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation citation_author _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID STRUCTURE_SUMMARY atom_site chem_comp em_entity_assembly em_entity_assembly_naturalsource entity entity_poly entity_poly_seq entity_src_gen entity_src_nat pdbx_poly_seq_scheme pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues struct_asym struct_conf struct_ref struct_ref_seq _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _em_entity_assembly.entity_id_list _em_entity_assembly.source _em_entity_assembly_naturalsource.strain _entity_src_gen.gene_src_strain _entity_src_gen.pdbx_host_org_strain _struct_asym.entity_id _struct_conf.beg_auth_comp_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_label_comp_id _struct_conf.end_label_seq_id _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.ref_id _struct_ref_seq.seq_align_end DATABASE_REFERENCES chem_comp_atom chem_comp_bond database_2 _database_2.pdbx_DOI _database_2.pdbx_database_accession STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name RCSB RCSB 2020-10-01 2021-01-06 2021-01-06 2025-06-04 Other private United States Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class with Sec62 Itskanov S Park E Sec61, translocon, endoplasmic reticulum, protein translocation, Sec62, Sec63, channel, PROTEIN TRANSPORT Itskanov S Kuo KM Gumbart JC Park E Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Nat.Struct.Mol.Biol. US 28 162 172 2021 33398175 doi:10.1038/s41594-020-00541-x 1545-9985 7kas FULLOVERLAP Endoplasmic reticulum protein-transport machinery Sec complex from yeast Endoplasmic reticulum protein-transport machinery Sec complex from yeast 0 1 2 3 4 5 6 7

Sec63 has the following mutations: E440R/F481S/del(441-447)

Saccharomyces cerevisiae BY4741 Protein transport protein SEC61 Saccharomyces cerevisiae BY4741 0.052978147999999996 1 LEVO MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETSDPLYWLRAMLASNRGTLLEL GVSPIITSSMIFQFLQGTQLLQIRPESKQDRELFQIAQKVCAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFA SLIVMLLDELLSKGYGLGSGISLFTATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTN LPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIMLQSALTSNIFLISQILFQKYPTNPLI RLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPIKTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGM VINGKRETSIYRELKKIIPTAAAFGGATIGALSVGSDLLGTLGSGASILMATTTIYGYYEAAAKEGGFTKNLVPGFSDLM P32915 Protein transport protein SSS1 Saccharomyces cerevisiae BY4741 0.008958641 1 LEVO MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIAVGIIGYAIKLIHIPIRYVIV P35179 Protein transport protein SBH1 Saccharomyces cerevisiae BY4741 0.008723155 1 Saccharomyces cerevisiae BY4741 LEVO MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFLAVGFIFSVVALHVISKVAGK LF P52870 Protein translocation protein SEC63 Saccharomyces cerevisiae BY4741 0.076312039 1 Saccharomyces cerevisiae BY4741 LEVO GGSGGSGGSGGSGGSPTNYEYDEASETWPSFILTGLLMVVGPMTLLQIYQIFFGANAEDGNSGKSKEFNEEVFKNLNEEY TSDEIKQFRRKFDKNSNKKSKIWSRRNIIIIVGWILVAILLQRINSNDAIKDAATKLFDPYEILGISTSASDRDIKSAYR KLSVKFHPDKLAKGLTPDEKSVMEETYVQITKAYESLTDELVRQNYLKYGHPDGPQSTSHGIALPRFLVDGSASPLLVVC YVALLGLILPYFVSRWWARTQSYTKKGIHNVTASNFVSNLVNYKPSEIVTTDLILHWLSFAHEFKQFFPDLQPTDFEKLL QDHINRRDSGKLNNAKFRIVAKCHSLLHGLLDIACGFRNLDIALGAINTFKCIVQAVPLTPNCQILQLPNVDKEHFITKT GDIHTLGKLFTLEDAKIGEVLGIKDQAKLNETLRVASHIPNLKIIKADFLVPGRPYISLKVLVRSAKQPLIPTSLIPEEN LTEPQDSESQRDPFAMMSKQPLVPYSFAPFFPTKRRGSWCCLVSSQKDGKILQTPIIIEKLSYKNLNDDKDFFDKRIKMD LTKHEKFDINDWEIGTIKIPLGQPAPETVGDFFFRVIVKSTDYFTTDLDITMNMKVRDSPAVEQVEVYSEEDDEYSTDDD ETESDDESDASDYTDIDTDTEAEDDESPEGENLYFQ P14906 Translocation protein SEC66 Saccharomyces cerevisiae BY4741 0.024263938999999998 1 LEVO MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKISEQPSIFDENDAHDLYFQIKE MSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLLYKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWV QLFVMVCKEICFNQALSRRYQSILKRKEVCIKEWELKINNDGRLVN P33754 Translocation protein SEC72 Saccharomyces cerevisiae BY4741 0.02163109 1 LEVO MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKGLFESGMKNLQQKKLNEALKN VSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILGKHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEAR ATCERGLALAPEDMKLRALLIETARNLAEYNGE P39742 Protein transport protein SEC62 Saccharomyces cerevisiae BY4741 ATCC 204508 / S288c 0.004783888 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) singleParticle particle 5 7.5 Quantifoil R1.2/1.3 GOLD 400 CARBON HOLEY GLOW DISCHARGE 35 AIR 0.039 ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 42017.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20 GATAN K3 (6k x 4k) 49.1 1 1274219

autopicked particles

Warp 1.0.7 cryoSPARC 2.12 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio reconstruction from cryoSPARC

C1 FOURIER SPACE 3.9 FSC 0.143 CUT-OFF cryoSPARC 2.12

Non-uniform refinement from cryoSPARC

119420 RANDOM ASSIGNMENT cryoSPARC 2.12 OTHER cryoSPARC 2.12

Non-uniform refinement from cryoSPARC

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