2025-05-28 REL RCSB INITIAL_RELEASE REPOSITORY RCSB RCSB 2024-09-18 2025-05-28 2025-05-28 2025-05-28 The G. Harold and Leila Y. Mathers Foundation 64395403 United States Damon Runyon Cancer Research Foundation DRG-2514-24 United States Cryo-EM structure of Tom1 (S. cerevisiae) Warner KM Hunkeler M Baek K Roy Burman SS Fischer ES transferase, ubiquitin, ubiquitylation complex Warner K Hunkeler M Baek K Schmoker A Roy Burman SS Overwijn D Jin C Donovan KA Fischer ES Structural ubiquitin contributes to K48 linkage specificity of the HECT ligase Tom1. Cell Rep US 44 115688 115688 2025 40359109 doi:10.1016/j.celrep.2025.115688 2211-1247 9dnt FULLOVERLAP Full length structure, S. cerevisiae Tom1 Full length structure, S. cerevisiae Tom1 0 1
Tom1 closed-ring conformation, stabilized
Saccharomyces cerevisiae 0.376 E3 ubiquitin-protein ligase TOM1 Saccharomyces cerevisiae 0.3774125 1 Trichoplusia ni LEVO MDWSHPQFEKSAVDENLYFQGGGRMVLFTRCEKARKEKLAAGYKPLVDYLIDCDTPTFLERIEAIQEWDRSRDDLYVWIP ILDRMDGLLLKVAEKYKYKQDPKKECEVKLVEMEAHDVDYCLKMLKFTRRLLLNTENRFVYSSGDVLMYLLNCPNFTIKL AVMRILAILGERFVIAREKIVAHNIFGDHNLRKKTLKLALSLSSSVMDEDGEHFSLVDLYFDKKKVPQKWRKLRFTHYTS NDFKKSSQQKNNINETQTSIKKVTMTTQELCEHSLQQIFDKGMALLPAESWFDFSIKASVAKAFSDDSGENIDLRNIIIE TKLNAIAFVNTIFSPPQVSSKLFELDPYAFNSLTDLISLSETKIPKELRTDALFTLECISLKHVWCSDIIRNLGGNISHG LLFQILRYIAKTLREATDEIDEEYNVRFFYLISNLADVKPLHESLFAAGLIPTLLEIVSIRNCPYKRTLASATHLLETFI DNSETTTEFIENDGFTMLITSVANEIDFTLAHPETWQPPKYSVVYYSISFRELAYIRSLLKLVLKLLSTDSGDRIRNLID SPILVSLKKILENKLVFGLTLITYTLDVVQKVINSEPTIYPVLVEAGLIPYVIDNFPKLIGPSAELLSLLPDVVSAICLN PEGLKQVKEKGLINNLFDFLLDADHARILTGGDRSTEYGTDIDELARHYPDLKANIVEALCNVIRKMPSTFRNEREFLFT SPKDQKYFFHRKNEEILTDKEEHEPAYWELLDKGTMLDTFTSVLFGMSLGNGSFSQVPQHLEARDFLAIIFMENPPYEYF TSVAISNVTEVLQYLDEKYEDYAFMDVMKVLNDQLENLNDFLNSPNDRSFFLERDGENSVRSCHSKLCRLAAILNIVTNV YIDLTTLSCKRIMQIYSYFDKRGFSLIKNLKLLFQKCALEEMYIRQHMPDSVITETMPLPIVDVSGDGPPLQIYIDDPKK GDQKGKITSVKTRNTLQMRTILYTLQSNTAILFRCFLRLSHSRNMDLEHKDLTTEVHIFENVVENVIEMLKATELEGHLP YILVLLNFNTFVFTIPKASPNSTEILQTIPAYIFYQKGGYLLYLHIIRDLFTRMTKIKDLSSLDNINYIDESNGILTLSC LINALTFYNKSMQTETMENVQSIGKYYVSIDDDYNIMKALTVPIKVMALAMILDLDKSDSLFKTQSRNVPYSVFKQLLSM LKNIFTNVNIYTKELYELHWDLIFPPIKKISLFEQVGIPGDVAANYLTDTGDDLPADNSIGLFSPEQWEKYKKLIGEDKS IYYPQPMQAQYYKGCSSKELDELRDTFFNDGLPSRIFTVLPFYPKLVNAFAKTLLQIFTKYDEPTEVFAGRILDRILETD LDDPATLSSLIHLFGIFLNEKYIYQKASHLMQRFIEYLEKSLKPEHVNTPWFSKALYVYEIILAKSELPHLEELSKDVLL RYPLLSMAKVFRIPDPMKQKLFDILIRVSDISNFYSALATSRILIFYSRDELYANNIARSGILSRLLKVIGSFQKLDKIN FLESSFLLLTRRCFETTENVDALIRAEINRSFTARPLGGGDDAVRELTTILEEKAHVVMRSPSQFIDVLCETARFHEFDD QGALVDYSLKRFLGEKDKNTQASSTEKSDIYERTGIMHLLLSQLMAASEKDWLSEPANSSDLPENKKAQLDPSRNPVCAY MIFLLKLLVELVSSYNQCKFEFLTFSRRNTYAERPRPRTTAINFFLYRLLDKPVGTDHDKHEAKRREVIGMLARSVIIGF LATVQDDRTTKTDVKLADPHMNFIRKFAIEAIIKAIRNATSSSKLLESNHLKLDMWFRIITSMVYVQAPYLRQLLDSNKV EADQYQLCKLVIDLGLPSVITEAMASIDLNYPFSKKIFNVAVEALNTISSTRNNFSEHFKIEDHDEVEDEVDESDKEEIP DMFKNSALGMYDVEDIEEDDDDDTSLIGDDDAMAFVDSDNGFEVVFSDEDDDMGEEDADDARSDSEENELSSEMQSSTAD GTDVDYEVDDADGLIINIDQPSGDDEEMADYDANISHSSHSENEDDASMDVIEVYDDELSSGYDVDLSDYDVDESDWDSG LSSLSISDEDSESSEDEPINSTRMGDSRRRWLIAEGVELTDDSQGESEEDDRGVFRGIEHIFSNENEPLFRVHDEMRHRN HHRSINRTHFHSAMSAPSLSLLNRGRRNQSNLINPLGPTGLEQVENDISDQVTVAGSGSRPRSHHLHFSEVLVSGSFFDE PVLDGIILKSTVSRWKDIFDMFYDSKTYANCIIPTVINRLYKVSLALQKDLENKREQEKLKNKNLLFNEAKVESHNSSDA ISVEQDDIQESNVTHDDHEPVYVTIQGSEVDIGGTDIDPEFMNALPDDIRADVFAQHVRERRAEARLNSDHNVHSREIDS DFLEAIPEDIREGILDTEAEEQRMFGRIGSSADVIRADDDVSNNDEEVENGLDHGNSNDRNNADPEKKKPARIYFAPLID RAGIASLMKSVFISKPYIQREIYHELFYRLCSSKQNRNDLMNTFLFILSEGIIDQHSLEKVYNIISSRAMGHAKTTTVRQ LPSDCTPLTVANQTIEILQSLIDADSRLKYFLIAEHDNLIVNKANNKSRKEALPDKKLRWPLWHLFSLLDRKLITDESVL MDLLTRILQVCTKTLAVLSTSSNGKENLSKKFHLPSFDEDDLMKILSIIMLDSCTTRVFQQTLNIIYNLSKLQGCMSIFT KHLVSLAISIMSKLKSALDGLSREVGTITTGMEINSELLQKFTLPSSDQAKLLKILTTVDFLYTHKRKEEERNVKDLQSL YDKMNGGPVWSSLSECLSQFEKSQAINTSATILLPLIESLMVVCRRSDLSQNRNTAVKYEDAKLLDFSKTRVENLFFPFT DAHKKLLNQMIRSNPKLMSGPFALLVKNPKVLDFDNKRYFFNAKLKSDNQERPKLPITVRREQVFLDSYRALFFKTNDEI KNSKLEITFKGESGVDAGGVTREWYQVLSRQMFNPDYALFLPVPSDKTTFHPNRTSGINPEHLSFFKFIGMIIGKAIRDQ CFLDCHFSREVYKNILGRPVSLKDMESLDPDYYKSLVWILENDITDIIEETFSVETDDYGEHKVINLIEGGKDIIVTEAN KQDYVKKVVEYKLQTSVKEQMDNFLVGFYALISKDLITIFDEQELELLISGLPDIDVDDWKNNTTYVNYTATCKEVSYFW RAVRSFDAEERAKLLQFVTGTSKVPLNGFKELSGVNGVCKFSIHRDFGSSERLPSSHTCFNQLNLPPYESYETLRGSLLL AINEGHEGFGLA Q03280 2.3.2.26 singleParticle particle 4.8 7.2 200.0 NaCl sodium chloride 30.0 HEPES HEPES 2.0 TCEP tris(2-carboxyethyl)phosphine 0.3 CHAPSO CHAPSO
30 mM HEPES pH 7.2, 200 mM NaCl, 2 mM TCEP, 0.3 mM CHAPSO
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ARRAY GLOW DISCHARGE AIR 0.039
60 seconds / hold time: 10 seconds / Current: 15 mA
 ETHANE 90 283.15 LEICA EM GP
CHAPSO detergent added to final conc. of 0.3 mM. Sample applied twice..
TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.1 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 11583 2.8 53.687 1 4216890 cryoSPARC 4.4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION Ab initio 3.0 FSC 0.143 CUT-OFF cryoSPARC 4.4.1 451216 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 emd_47058.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -0.054910924 0.16823931 0.00029232216 0.005334613 0.83 0.83 0.83 0.03 AUTHOR Tom1-BS3, consensus map AlphaFold in silico model 121.0 emd_47058_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -0.0018290818 1.872214 0.0012287613 0.025006913 0.83 0.83 0.83 AUTHOR Tom1-BS3, deepEMhancer sharpened emd_47058_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -0.14198668 0.19019638 0.0003068981 0.015242068 0.83 0.83 0.83 AUTHOR Tom1-BS3, half map A emd_47058_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -0.12547165 0.19135898 0.000307091 0.015244518 0.83 0.83 0.83 AUTHOR Tom1-BS3, half map B