2025-05-28 REL RCSB 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 map of Tom1 ubiquitylation, class 6 Warner KM Hunkeler M Baek K 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 Class 6 Ternary complex of E3 ubiquitin ligase Tom1 with E2 ubiquitin conjugating enzyme UBE2D2 and ubiquitin Class 6 Ternary complex of E3 ubiquitin ligase Tom1 with E2 ubiquitin conjugating enzyme UBE2D2 and ubiquitin 0 1 2 3
Complex identified by plunge-freezing Tom1 in active ubiquitylation cascade
Saccharomyces cerevisiae 0.44 E3 ubiquitin-protein ligase Tom1 Saccharomyces cerevisiae
StrepIItag-TEV-Tom1 fusion
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 E2 ubiquitin-conjugating enzyme UBE2D2 Homo sapiens
TEV cleavage product GST-TEV-UBE2D2
Escherichia coli LEVO GSMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNI NSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM P62837 6.3.2.19 Polyubiquitin-C Homo sapiens
Ubiquitin
Escherichia coli LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG P0CG48 singleParticle particle 1.9 7.2 100.0 NaCl sodium chloride 15.0 HEPES HEPES 1.0 TCEP tris(2-carboxyethyl)phosphine 0.1 CHAPSO CHAPSO 1.0 Mg-ATP Magnesium Adenosine triphosphate 0.5 Commercial E3 Ligase Reaction Buffer (R&D Systems)
1.5 mM HEPES pH 7.2, 100 mM NaCl, 1 mM TCEP, 0.1 mM CHAPSO, 1 mM Mg-ATP, 0.5X E3 Ligase Reaction Buffer (R and D biosystems)
 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 PLUNGER
CHAPSO detergent added to final application at indicated concentration. Sample applied twice..
UBA1 and UBE2D2 were pre-charged for 20 minutes at room temperature in a solution containing 0.5 uM UBA1, 18 uM UBE2D2, 2 mM Mg-ATP (R and D Systems) and 25 uM ubiquitin (R and D Systems), buffered with 1X E3 Ligase Reaction Buffer (R and D Systems). Separately, Tom1 was pre-incubated with histone H2B at room temperature at room temperature for 20 minutes at a concentration of 8 uM Tom1 and 16 uM histone H2B. Samples were pre-mixed at a one-to-one volume-volume ratio for 45 seconds and 90 seconds, before addition of detergent and immediate sample application (final sample concentration: 4 uM Tom1, 8 uM histone H2B, 0.25 uM UBA1, 9 uM UBE2D2, 1 mM Mg-ATP, 12.5 uM ubiquitin, 0.2 mM CHAPSO).
 TFS TALOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 2.2 36000.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 (6k x 4k) 1 8592 4.993 52.55 1 3159343 cryoSPARC 4.4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION
Data collected from previous EM session
 C1 4.0 FSC 0.143 CUT-OFF cryoSPARC 4.4.1 49235 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 emd_47054.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 316.80002 316.80002 316.80002 90.0 90.0 90.0 X Y Z -0.18926425 0.57487005 -0.00038141475 0.026379818 1.32 1.32 1.32 0.119 AUTHOR consensus, Tom1 ubiquitylation class 6 AlphaFold in silico model 121.0 emd_47054_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 316.80002 316.80002 316.80002 90.0 90.0 90.0 X Y Z -0.3797624 0.78636473 0.0008892914 0.04807167 1.32 1.32 1.32 AUTHOR half map A, Tom1 ubiquitylation class 6 emd_47054_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 316.80002 316.80002 316.80002 90.0 90.0 90.0 X Y Z -0.3513076 0.727904 0.0009189164 0.04807753 1.32 1.32 1.32 AUTHOR half map B, Tom1 ubiquitylation class 6