Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map)

2026-05-27 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-01-09 2026-05-27 2026-05-27 2026-05-27 Austrian Research Promotion Agency 852936 Austria H2020 Marie Curie Actions of the European Commission 847548 European Union Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map) Grabarczyk DB Clausen T Ubiquitin ligase Protein quality control, LIGASE Grabarczyk DB Ehrmann JF Murphy P Kurzbauer R Bell LE Deszcz L Neuhold J Schleiffer A Shulkina A Versteeg GA Meinhart A Zavodszky E Hegde RS Clausen T Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control To Be Published 0353 EMD-52504 consensus EM volume EMD-52506 focused EM volume EMD-52511 focused EM volume EMD-52513 focused EM volume EMD-52515 focused EM volume EMD-52516 focused EM volume 9hyf FULLOVERLAP EMDB EMD-52502 associated EM volume

EMDB EMD-52504 consensus EM volume EMDB EMD-52506 focused EM volume EMDB EMD-52511 focused EM volume EMDB EMD-52513 focused EM volume EMDB EMD-52515 focused EM volume EMDB EMD-52516 focused EM volume UBR4/KCMF1 ubiquitin ligase complex UBR4/KCMF1 ubiquitin ligase complex 0 1 2 Caenorhabditis elegans UBR-type domain-containing protein Caenorhabditis elegans 0.441954656 2 Trichoplusia ni LEVO MDPRETAIGLVRYVTENAAKDFDGESIAAIIYRLRVVENYVSSDVDIICEAMRILIKKLVNLPPITFSPDVWMPIMTSIT EGAIEPQWRIMMESIDISKFSSTSSNFVHMDSITASSTKCSEQITSICKGFALEFGLTRRLFSAIWNTDLEETARKMMNQ EWDSVKIDSSPDSAKQAAGLIEKSIFDLFSEMKDHETFANELYYAALARILNNSRRLQENKKPAIQDSEDISFYESSLHI YDELIKKLWPHLSKKDPNVKKNTLIIFEKLISLSPTDVLVQRITEKFIDSCEWLKISGEEICTSMEPRLWKIVGSLVSRI LDLKKTIPYEIVSYAIAVHITQEVTLASPEVSDCGPDSFDSTCDQPSNMKERFLRHMVDSYFQTRSSLLSIIQFLRTAKS SEEIVQFMRVFYPELVFGNETLITHAAIEMLRESASHHSIKADDFISIVLSVIDAPAIVRIIDVISCIKDEKVRKEAVEK TIIRMANDLEDEDQKREGYVNHLHENGSFWNDIAKYADASILDKAGKRFVEVSVDSMDIRSSVLATDIFLTILKLKLTSE AEREPESCVICNVSYSNIKIDLEKWNKMGNILVECNMVKRSKSEALPLFTIHQLENIDLPMRDLVYVVTQMKFLDTKEGM ELHRKFYDGLPGVNVIFEKFMSKSHKIELCMKLLDEFAKIIAINEKSLIFSLDHENILDWLEEIGVLDSPQITEKLVDIC FSIEVWDVLTLLQLDGPECHYWDLQMFGRFWKTSLMDLLDEKMMKKVNEKMGSILKEQYDKQSHVAKATREKRSNGKFPN RPKVADWEEQLLLMHNRIAGHLTKKKVEDFADESTQKFTWLLGVCSGQMSYKKEVAVDAEKILSRLYPDAEKRNEVLYHF GVSSILKGLDRPRGKLSLHILFMQIYLDLVQIDSKSWKIDDSVQKLSRRLGGFNEWLMIVDEEKREDDGGFRIYIVLNLS HYFWELLEGCKASQVVDAHAILKIRKFAEVLASILDKITFWPNPKLHAYYYIAQFLEPLETIFHFPEIAEQNRKVIESFF KQLFDKLLEQKYQEGLLQDTKLIIQKTDKYLSSSLNLFNEYNTQEPSKIYPVNEIFSLFCRYGSENVHLYCLKMIKKSLQ TLASNILEHEHILKGEVCIETELQKRLVCDAVLLTEFFGYFSCIYAQVSENQPSEHDDVAKAFMLLDSDIHLKTKSRKRS TQNSVAVGSHRHQTAENMDLNFCTYKSTGRAYVTQHWYNCYTCNMMESEGVCSVCAINCHRGHDLAYSKKGSFFCDCGEK KCGAMQGIYHLPNSMYSLRGQLPEKNGDKTLPKIRNVFEHRFENLNSNCCDELKSALNDVQEEFKEVQDDLEQILEAVDF ANQKALQVTEERLAVLESFNDMDDVIISEKEKFIEPLESGHFLPTRRDDLPVQELRVASSQHKIRELSDIIKLDDGTELL VLIPESIQTCLQLHYMDTRTNLIQGMHALRTETEQIPFNARSLHVSGNRLVVCGQYEFFALRFSPQGDVIDRAHIKLLEN GASSSMNNNPVVRAKFCREIESDKRRRQLIAVATMQYIRIYDLTLHETNFVEEMVLPAGNVEDVEIINQEDGNVRILVLS SSGYLYEHNISVFNAENNSIFLTNVVNTPGMDMNGDGVSLHYSSTFNLLFVSLENGAFVAQLPEPTGNSTAPIYDWKHLN IKNPVDAWKETSGIIACLSTNCNHQVNYFHPTVGKILLQKTSVKRSIMTYFLMTSAKNQSVYSVLIYPNVPTCEIWETSW NNVHDLWIDDVPTERYAVEVVEQKSTQIPIDRDELVLLAEQCEQIRTVDWNCREIGMFYTHEELNNRLSSSDSLPITLIQ QTHFKLSARITNFRQIVRMIRVEVEGNTGPEYLKIGTTRYSISSRGPKTFDLRLSREESLALDHRDITIEVIPRSNQNRV TLKSLRLLGCDRSAMDEIQPRYERQPILTNSNKLVYSILEFATLSGLEWAGNMAKKHLSRKLNHPAVCSVSTRAIVKCHP SVDEELFKIIDGAYLQEWKALIDWTESEGFGEMRLHHVEQLLDRMEAVRTRWPYFVKSLKREFGTVTSFVELMRNEMKRM PLHRCQMMAQAIVKIVFGLLSNGTNEAEQLIHVFLNIFTDQDTYHLANDMRSAVQETISRFENALKEEKKLMVEHENMDK ESVLRIKNYGFSPFYGAPRIIAKTPESMLIAKIAETIPIDSEENFKWLEQLISMILEKLTRSNSTVTWQNLSDSPSYNLS RVLASCLAICDPVIIRNHFSRLIHIIKYDVEKIFPMSEKSYSNYSLLRSVELLLFVCLEKRGDESKENQEMLDSIVHDLQ AVGIRNLCLKILEKVIPHWKDRGPSTFSRNSAESRKVWLPHVPLVSSSANPPNTSIMNWPSTSEDSYIIACTDLILLIPQ HLQELDRRKSVPRDDQWIQKLCQLASLSSGCSAYRQCKKLLLAMCHNDENKYKIMRDKYKMQDLLQQLVKKYLDVSKEVG GHQQLTEIVDVLASITKLALIRPDMWRDVCSTHTTWLLRLACYTTDVVASQVVELLIVAVRDSSVGGQLSIQLADSIVEA ENGEFIEKIIKRFLIGRDEQLRWTLHGMLRSVIQLASRQNQCILVKKLYNTIYPLAANLGVQGAQLVDLIATYAPRVFSS TELVAMTQSEISTIEKIRNTLNGDGYQGMYKLMSDLGLGWKSINFDRNPCLVCFTSKGSHDVVKMTSIKSDIRYSANTII YKLISNYEVSKVTIKLTELKKSKSIKKVSLYYSAKSVESVDLKLHPELWRKCAMVTVAENETVINLSLAVPVVTSSLIVE FEEVVDHRGSSQLHCPRCTVPVRTHSGVCESCGENAFQCAKCRAINYVEKEPFLCQSCGFCKYAQISLFVVCRALPGAQH ITCDAERGQCVQEITQLLIKMETTKTKLTGYRAACESLYLRNRPLPPYKLHVENNHTSEFFDANGTMNIEQLPFQSITMP MNNLAVAIRTLHSELCQQTQQLMYLHEELNRYDHASEVSVVFHKPQNISYYSTGQSCFGCLCNQLLHSVALLHSSCDDEN ALNLILSSDSLIEKLGVLAQTYETLREEVEELLVRLMFDRLDVTTKVEKLIHTGDINLSVMVKSLMYAADPTWQQKLKLL IRLAMDKRDENCCLQALMVLSKYLEATKSVTLDERKKIKLTPNKNITKWLTTDEEWKDCFSVASTSTAPTKSLPSNPYQW ITDCLFSQWMSVRSAANQLLVNLSRQQFHEPVALLILCENMSKLSDVPSSVCDQFMCSAHTIIDSSVNTKARLFVQQFHV YLIKRIHEECAKLHEQSVNLLSDNMFGERLRCFVELLSLLLSGSNVENVLLKAGADDLLIFLLHSTIFLKRIMTRRTRAT DSSRIALEKLLKRVSCRDGTKLMSVCVESLKLVKDTSTLGIIVGVMMEIMDPQQETEESFLIQIEKDIAQEDFLQGRMTH NPYNSSDPGMGPLMRDIKNKICRDTEMIALMEDDNGMELLVNGNIISLSLSVRDVYDRLWKRSNNGSPMLIVYRMRGLMG DAVETFIENFGVADNSEADDEEDEQLVRMTHCLMECGGIDKLMDLLTTNVDSSSGRFLLCYLRKIFERIVKIPIGRKILV QRRMVERMMSVIRTCCADPTNESKVLIGMELYKVVEFVVSDKHVQDILGGIREDDAMWWFDLFEKRGNEEGSVTELHRKT AQILDQMTMSIGNIVLGNDASEGVLVKMYEKVLKWEQIDSGAPPSGATDHQNRSRITKKDQIMLMTEQLATITSNIISSA HGIRLKQKILDSGVISSTCNYLTKDLPNLYQPTESPEWKVFLARPSLKLILTLLAGLARGHQASQKEIAKTTLKLMHRLE QVASDNSIGTLAENVIEALNE A0A0S4XR36 E3 ubiquitin-protein ligase kcmf-1 Caenorhabditis elegans 0.057890016 2 Trichoplusia ni LEVO MVTPLTGTHEGVSCDGCAFTAFAGNRYKCLRCSDYDLCFSCFTTKNYGDQQTIADIPIHDESHPMQLILSSVDFDLVYQG DPTRHYDERKIVSFTCPYCNITGLTERQFGTHVLSQHPEAPGYSVICPLCIGNTEMEHIQSKETENLSVHWTEIHLHTME NLFRSTEPITTRPVQRRPMLARRGNRAGVSRTAAQGRPLQDEIGAEMAALLRNMGPDSVEDIRRFTEMMTVPLLPGIRSS QRLMTSTGDRPTVVVESAVTHQDPNVQQVIRPLATIPIYPPTSDESGDETPQPAADSADESEDDNDIQELDDMQPIVEDE ALKKDEFWKTLKTRISEEDVDLILETMKSTAKVKEDIDDKMPVWTQRPLKRLANAAQVTTTSDSEGDPGWLPLSFETTPI RSTGCGGYWSDKRFLRPRKMQREQSVASSNAEIMEKAEIALALIRASCLHEPVFTDPTKPDIALKEALQHLRLGEKPAKM MEYQAAEELVNMPERDPITTGEMEVEIPDFTARGY P34664 2.3.2.27 ZINC ION 6.5409e-05 18 ZN singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.0 FEI FALCON IV (4k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.0 FSC 0.143 CUT-OFF 691759 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_52502.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 486.912 486.912 486.912 90.0 90.0 90.0 X Y Z 0.0 0.05380428 0.009822927 0.00064411643 1.268 1.268 1.268 0.0104 AUTHOR ::::EMDATABANK.org::::EMD-52502::::