CryoEM structure of the Chaetomium thermophilum TOM holo complex at 3.2 angstrom resolution (pALDH treated)

2025-07-30 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update PDBe PDBe 2025-02-01 2025-07-09 2025-07-09 2025-07-30 Max Planck Society Germany CryoEM structure of the Chaetomium thermophilum TOM holo complex at 3.2 angstrom resolution (pALDH treated) Agip ANA Ornelas P Yang TJ Ermanno U Haeder S McDowell MA Kuehlbrandt W Mitochondria, MEMBRANE PROTEIN Agip AA Ornelas P Yang TJ Uboldi E Hader S McDowell MA Kuhlbrandt W Structures of Chaetomium thermophilum TOM complexes with bound preproteins. Proc.Natl.Acad.Sci.USA US 122 e2507279122 e2507279122 2025 40674418 doi:10.1073/pnas.2507279122 1091-6490 0040 PNASA6 9i7s FULLOVERLAP TOM TOM 0 1 2 3 4 5 6 Thermochaetoides thermophila DSM 1495 0.179 Mitochondrial import receptor subunit tom22 Thermochaetoides thermophila DSM 1495 0.019237748

Linker & FLAG fused to the C-terminus of Tom22.

2 Thermochaetoides thermophila DSM 1495 LEVO MVQLVEVEDEHFTQPQPGPEEDDDEYTDTDSEISTESNFDPSEETLADRLHALRDMVPPAYRGWIYHKYEQTTSAVRKAL SFAGRAAWTVSVTALLVGVPFSLAYGEDQQYAAMEQEQRMRELGGEVLTAGAPGSQGGGLTAEQVNAALGRSEAKPALGS DYKDHDGDYKDDDDK G0S6L5 Mitochondrial import receptor subunit Tom5 Thermochaetoides thermophila DSM 1495 0.005345149999999999 2 LEVO MFGGCQPPQPSPEELRAAEAEAASTIQRAIATAAVLYLAPFIVDAVYKMF Mitochondrial import receptor subunit tom6 Thermochaetoides thermophila DSM 1495 0.009008387 2 LEVO MPPKRVSYNSRRSLNPITGAYNALFVSENASIVRSVVAFGLAVTFLASGWAEAILSCVPSPLVSSRQQQPPLTDLQKPCV NGLI G0S9G0 Import receptor subunit-like protein Thermochaetoides thermophila DSM 1495 0.008110613999999999

Mitochondrial import receptor subunit Tom7

2 LEVO MLALSEESKVRRGPSLRTIRLGADSKQERISKLIEISRVVIHYGYLPMILYLGYTRSEPKPSIIRLLSPLS G0SE07 Tom20 Thermochaetoides thermophila DSM 1495 0.020228916

Mitochondrial import receptor subunit Tom20

2 LEVO MSSSPSPAIVATAAVATLAAGVLAYAAYFDYQRRHNAEFRRQLRRNERRQARAEKDLAEASAKAQRQRIKQAVDEAKEEG FPTSAEDKEAFFLEQVQAGEMMSADPSKHLEAALCFYKALKVYPTPGDLINIYDKTVSKPILDILAEMIAYDSSLRIGTA YTGPAGVDVADLMREMGAVPGVGLD G0S6E4 Mitochondrial import receptor subunit (Tom40)-like protein Thermochaetoides thermophila DSM 1495 0.03784960899999999

Mitochondrial import receptor subunit Tom40

2 LEVO MASSTNSPLAFLRSNPVFASLSDLYDAFQERRQKLGLSNPGLVENIAKEVQRDVLTTNLMFSGLRADLTKAFSLNPLFQV SHQFAMGERLSPYTFAALYGTSKMFAQGNIDDQGNLSTTFNYRWTPSFTTKTRFQITPGATGQDMAQFEHEYSGADFTAT IKALNPSFLEGGLTGIFVGQYLQSITPKLSLGLEAVWQRAGLTQGPDTAISYVGRYKTENWIASAQLQAQGALNASYWQR LGEKVQAGVDMTLSVNPGAAMMGGPTKEGITTFGAKYDFRMSTFRAQIDTKGKLSCVLEKRVAAPVMMTFAADVDHFTQQ AKVGVGISIEAGGEELQDQQPAPNIPF G0S7S2 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007901449999999999 10 PC1 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol 0.0005167519999999999 8 DU0 DIUNDECYL PHOSPHATIDYL CHOLINE 0.000622834 1 PLC singleParticle particle 1.9 8.0 50.0 K2HPO4/KH2PO4 Potassium Phosphate Buffer 50.0 KCl Potassium Chloride 1.0 EDTA Ethylenediaminetetraacetic acid 1.0 TCEP Tris (2-carboxyethyl) phosphine 0.02 GDN Glyco-diosgenin Quantifoil R2/2 COPPER 300 GLOW DISCHARGE 90 AIR 0.04

ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.6 2.4 215000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 4096 4096 34438 3.0 70.0 1 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION C2 FOURIER SPACE 3.2 FSC 0.143 CUT-OFF cryoSPARC 51299 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_52660.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 320.88 320.88 320.88 90.0 90.0 90.0 X Y Z -0.316967 0.5428492 0.0004105436 0.008664235 0.573 0.573 0.573 0.043 AUTHOR ::::EMDATABANK.org::::EMD-52660:::: Full map generated by cryoSPARC Other in silico model

ModelAngelo

AlphaFold in silico model

AlphaFold3

AB INITIO MODEL

A combination of ModelAngelo and AlphaFold3

REAL emd_52660_msk_1.map emd_52660_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 320.88 320.88 320.88 90.0 90.0 90.0 X Y Z -0.1341458 0.26051357 0.00034150912 0.005376457 0.573 0.573 0.573 AUTHOR ::::EMDATABANK.org::::EMD-52660:::: Full map with a -10 b-factor applied to it using cryoSPARC emd_52660_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 320.88 320.88 320.88 90.0 90.0 90.0 X Y Z -0.24155934 0.33199963 0.00034532297 0.026106138 0.573 0.573 0.573 AUTHOR ::::EMDATABANK.org::::EMD-52660:::: Half map A generated by cryoSPARC emd_52660_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 320.88 320.88 320.88 90.0 90.0 90.0 X Y Z -0.22823282 0.35913387 0.0003513537 0.026159588 0.573 0.573 0.573 AUTHOR ::::EMDATABANK.org::::EMD-52660:::: Half map B generated by cryoSPARC