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FASTA Sequence PDB Format mmCIF Format
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9HYF

Cryo-em structure of the c. elegans ubr4/kcmf1 complex (composite map)

PDB DOI: 10.2210/pdb9hyf/pdb

Classification: LIGASE
Organism(s): Caenorhabditis Elegans

Deposited: 2025-01-09
Deposition Author(s): Clausen, T. , Grabarczyk, D.B.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.0 Å

9hyf
Literature

Cryo-em structure of the c. elegans ubr4/kcmf1 complex (composite map)

Clausen, T. , Grabarczyk, D.B.

Primary Citation of Related Structures: 9HYF


Proteins
Molecule Chains Sequence Length Organism Sequence
UBR-type domain-containing protein A 3861 Caenorhabditis Elegans MDPRETAIGLVRYVTENAAKDFDGESIAAIIYRLRVVENYVSSDVDIICEAMRILIKKLVNLPPITFSPDVWMPIMTSITEGAIEPQWRIMMESIDISKFSSTSSNFVHMDSITASSTKCSEQITSICKGFALEFGLTRRLFSAIWNTDLEETARKMMNQEWDSVKIDSSPDSAKQAAGLIEKSIFDLFSEMKDHETFANELYYAALARILNNSRRLQENKKPAIQDSEDISFYESSLHIYDELIKKLWPHLSKKDPNVKKNTLIIFEKLISLSPTDVLVQRITEKFIDSCEWLKISGEEICTSMEPRLWKIVGSLVSRILDLKKTIPYEIVSYAIAVHITQEVTLASPEVSDCGPDSFDSTCDQPSNMKERFLRHMVDSYFQTRSSLLSIIQFLRTAKSSEEIVQFMRVFYPELVFGNETLITHAAIEMLRESASHHSIKADDFISIVLSVIDAPAIVRIIDVISCIKDEKVRKEAVEKTIIRMANDLEDEDQKREGYVNHLHENGSFWNDIAKYADASILDKAGKRFVEVSVDSMDIRSSVLATDIFLTILKLKLTSEAEREPESCVICNVSYSNIKIDLEKWNKMGNILVECNMVKRSKSEALPLFTIHQLENIDLPMRDLVYVVTQMKFLDTKEGMELHRKFYDGLPGVNVIFEKFMSKSHKIELCMKLLDEFAKIIAINEKSLIFSLDHENILDWLEEIGVLDSPQITEKLVDICFSIEVWDVLTLLQLDGPECHYWDLQMFGRFWKTSLMDLLDEKMMKKVNEKMGSILKEQYDKQSHVAKATREKRSNGKFPNRPKVADWEEQLLLMHNRIAGHLTKKKVEDFADESTQKFTWLLGVCSGQMSYKKEVAVDAEKILSRLYPDAEKRNEVLYHFGVSSILKGLDRPRGKLSLHILFMQIYLDLVQIDSKSWKIDDSVQKLSRRLGGFNEWLMIVDEEKREDDGGFRIYIVLNLSHYFWELLEGCKASQVVDAHAILKIRKFAEVLASILDKITFWPNPKLHAYYYIAQFLEPLETIFHFPEIAEQNRKVIESFFKQLFDKLLEQKYQEGLLQDTKLIIQKTDKYLSSSLNLFNEYNTQEPSKIYPVNEIFSLFCRYGSENVHLYCLKMIKKSLQTLASNILEHEHILKGEVCIETELQKRLVCDAVLLTEFFGYFSCIYAQVSENQPSEHDDVAKAFMLLDSDIHLKTKSRKRSTQNSVAVGSHRHQTAENMDLNFCTYKSTGRAYVTQHWYNCYTCNMMESEGVCSVCAINCHRGHDLAYSKKGSFFCDCGEKKCGAMQGIYHLPNSMYSLRGQLPEKNGDKTLPKIRNVFEHRFENLNSNCCDELKSALNDVQEEFKEVQDDLEQILEAVDFANQKALQVTEERLAVLESFNDMDDVIISEKEKFIEPLESGHFLPTRRDDLPVQELRVASSQHKIRELSDIIKLDDGTELLVLIPESIQTCLQLHYMDTRTNLIQGMHALRTETEQIPFNARSLHVSGNRLVVCGQYEFFALRFSPQGDVIDRAHIKLLENGASSSMNNNPVVRAKFCREIESDKRRRQLIAVATMQYIRIYDLTLHETNFVEEMVLPAGNVEDVEIINQEDGNVRILVLSSSGYLYEHNISVFNAENNSIFLTNVVNTPGMDMNGDGVSLHYSSTFNLLFVSLENGAFVAQLPEPTGNSTAPIYDWKHLNIKNPVDAWKETSGIIACLSTNCNHQVNYFHPTVGKILLQKTSVKRSIMTYFLMTSAKNQSVYSVLIYPNVPTCEIWETSWNNVHDLWIDDVPTERYAVEVVEQKSTQIPIDRDELVLLAEQCEQIRTVDWNCREIGMFYTHEELNNRLSSSDSLPITLIQQTHFKLSARITNFRQIVRMIRVEVEGNTGPEYLKIGTTRYSISSRGPKTFDLRLSREESLALDHRDITIEVIPRSNQNRVTLKSLRLLGCDRSAMDEIQPRYERQPILTNSNKLVYSILEFATLSGLEWAGNMAKKHLSRKLNHPAVCSVSTRAIVKCHPSVDEELFKIIDGAYLQEWKALIDWTESEGFGEMRLHHVEQLLDRMEAVRTRWPYFVKSLKREFGTVTSFVELMRNEMKRMPLHRCQMMAQAIVKIVFGLLSNGTNEAEQLIHVFLNIFTDQDTYHLANDMRSAVQETISRFENALKEEKKLMVEHENMDKESVLRIKNYGFSPFYGAPRIIAKTPESMLIAKIAETIPIDSEENFKWLEQLISMILEKLTRSNSTVTWQNLSDSPSYNLSRVLASCLAICDPVIIRNHFSRLIHIIKYDVEKIFPMSEKSYSNYSLLRSVELLLFVCLEKRGDESKENQEMLDSIVHDLQAVGIRNLCLKILEKVIPHWKDRGPSTFSRNSAESRKVWLPHVPLVSSSANPPNTSIMNWPSTSEDSYIIACTDLILLIPQHLQELDRRKSVPRDDQWIQKLCQLASLSSGCSAYRQCKKLLLAMCHNDENKYKIMRDKYKMQDLLQQLVKKYLDVSKEVGGHQQLTEIVDVLASITKLALIRPDMWRDVCSTHTTWLLRLACYTTDVVASQVVELLIVAVRDSSVGGQLSIQLADSIVEAENGEFIEKIIKRFLIGRDEQLRWTLHGMLRSVIQLASRQNQCILVKKLYNTIYPLAANLGVQGAQLVDLIATYAPRVFSSTELVAMTQSEISTIEKIRNTLNGDGYQGMYKLMSDLGLGWKSINFDRNPCLVCFTSKGSHDVVKMTSIKSDIRYSANTIIYKLISNYEVSKVTIKLTELKKSKSIKKVSLYYSAKSVESVDLKLHPELWRKCAMVTVAENETVINLSLAVPVVTSSLIVEFEEVVDHRGSSQLHCPRCTVPVRTHSGVCESCGENAFQCAKCRAINYVEKEPFLCQSCGFCKYAQISLFVVCRALPGAQHITCDAERGQCVQEITQLLIKMETTKTKLTGYRAACESLYLRNRPLPPYKLHVENNHTSEFFDANGTMNIEQLPFQSITMPMNNLAVAIRTLHSELCQQTQQLMYLHEELNRYDHASEVSVVFHKPQNISYYSTGQSCFGCLCNQLLHSVALLHSSCDDENALNLILSSDSLIEKLGVLAQTYETLREEVEELLVRLMFDRLDVTTKVEKLIHTGDINLSVMVKSLMYAADPTWQQKLKLLIRLAMDKRDENCCLQALMVLSKYLEATKSVTLDERKKIKLTPNKNITKWLTTDEEWKDCFSVASTSTAPTKSLPSNPYQWITDCLFSQWMSVRSAANQLLVNLSRQQFHEPVALLILCENMSKLSDVPSSVCDQFMCSAHTIIDSSVNTKARLFVQQFHVYLIKRIHEECAKLHEQSVNLLSDNMFGERLRCFVELLSLLLSGSNVENVLLKAGADDLLIFLLHSTIFLKRIMTRRTRATDSSRIALEKLLKRVSCRDGTKLMSVCVESLKLVKDTSTLGIIVGVMMEIMDPQQETEESFLIQIEKDIAQEDFLQGRMTHNPYNSSDPGMGPLMRDIKNKICRDTEMIALMEDDNGMELLVNGNIISLSLSVRDVYDRLWKRSNNGSPMLIVYRMRGLMGDAVETFIENFGVADNSEADDEEDEQLVRMTHCLMECGGIDKLMDLLTTNVDSSSGRFLLCYLRKIFERIVKIPIGRKILVQRRMVERMMSVIRTCCADPTNESKVLIGMELYKVVEFVVSDKHVQDILGGIREDDAMWWFDLFEKRGNEEGSVTELHRKTAQILDQMTMSIGNIVLGNDASEGVLVKMYEKVLKWEQIDSGAPPSGATDHQNRSRITKKDQIMLMTEQLATITSNIISSAHGIRLKQKILDSGVISSTCNYLTKDLPNLYQPTESPEWKVFLARPSLKLILTLLAGLARGHQASQKEIAKTTLKLMHRLEQVASDNSIGTLAENVIEALNE
UBR-type domain-containing protein B 3861 Caenorhabditis Elegans MDPRETAIGLVRYVTENAAKDFDGESIAAIIYRLRVVENYVSSDVDIICEAMRILIKKLVNLPPITFSPDVWMPIMTSITEGAIEPQWRIMMESIDISKFSSTSSNFVHMDSITASSTKCSEQITSICKGFALEFGLTRRLFSAIWNTDLEETARKMMNQEWDSVKIDSSPDSAKQAAGLIEKSIFDLFSEMKDHETFANELYYAALARILNNSRRLQENKKPAIQDSEDISFYESSLHIYDELIKKLWPHLSKKDPNVKKNTLIIFEKLISLSPTDVLVQRITEKFIDSCEWLKISGEEICTSMEPRLWKIVGSLVSRILDLKKTIPYEIVSYAIAVHITQEVTLASPEVSDCGPDSFDSTCDQPSNMKERFLRHMVDSYFQTRSSLLSIIQFLRTAKSSEEIVQFMRVFYPELVFGNETLITHAAIEMLRESASHHSIKADDFISIVLSVIDAPAIVRIIDVISCIKDEKVRKEAVEKTIIRMANDLEDEDQKREGYVNHLHENGSFWNDIAKYADASILDKAGKRFVEVSVDSMDIRSSVLATDIFLTILKLKLTSEAEREPESCVICNVSYSNIKIDLEKWNKMGNILVECNMVKRSKSEALPLFTIHQLENIDLPMRDLVYVVTQMKFLDTKEGMELHRKFYDGLPGVNVIFEKFMSKSHKIELCMKLLDEFAKIIAINEKSLIFSLDHENILDWLEEIGVLDSPQITEKLVDICFSIEVWDVLTLLQLDGPECHYWDLQMFGRFWKTSLMDLLDEKMMKKVNEKMGSILKEQYDKQSHVAKATREKRSNGKFPNRPKVADWEEQLLLMHNRIAGHLTKKKVEDFADESTQKFTWLLGVCSGQMSYKKEVAVDAEKILSRLYPDAEKRNEVLYHFGVSSILKGLDRPRGKLSLHILFMQIYLDLVQIDSKSWKIDDSVQKLSRRLGGFNEWLMIVDEEKREDDGGFRIYIVLNLSHYFWELLEGCKASQVVDAHAILKIRKFAEVLASILDKITFWPNPKLHAYYYIAQFLEPLETIFHFPEIAEQNRKVIESFFKQLFDKLLEQKYQEGLLQDTKLIIQKTDKYLSSSLNLFNEYNTQEPSKIYPVNEIFSLFCRYGSENVHLYCLKMIKKSLQTLASNILEHEHILKGEVCIETELQKRLVCDAVLLTEFFGYFSCIYAQVSENQPSEHDDVAKAFMLLDSDIHLKTKSRKRSTQNSVAVGSHRHQTAENMDLNFCTYKSTGRAYVTQHWYNCYTCNMMESEGVCSVCAINCHRGHDLAYSKKGSFFCDCGEKKCGAMQGIYHLPNSMYSLRGQLPEKNGDKTLPKIRNVFEHRFENLNSNCCDELKSALNDVQEEFKEVQDDLEQILEAVDFANQKALQVTEERLAVLESFNDMDDVIISEKEKFIEPLESGHFLPTRRDDLPVQELRVASSQHKIRELSDIIKLDDGTELLVLIPESIQTCLQLHYMDTRTNLIQGMHALRTETEQIPFNARSLHVSGNRLVVCGQYEFFALRFSPQGDVIDRAHIKLLENGASSSMNNNPVVRAKFCREIESDKRRRQLIAVATMQYIRIYDLTLHETNFVEEMVLPAGNVEDVEIINQEDGNVRILVLSSSGYLYEHNISVFNAENNSIFLTNVVNTPGMDMNGDGVSLHYSSTFNLLFVSLENGAFVAQLPEPTGNSTAPIYDWKHLNIKNPVDAWKETSGIIACLSTNCNHQVNYFHPTVGKILLQKTSVKRSIMTYFLMTSAKNQSVYSVLIYPNVPTCEIWETSWNNVHDLWIDDVPTERYAVEVVEQKSTQIPIDRDELVLLAEQCEQIRTVDWNCREIGMFYTHEELNNRLSSSDSLPITLIQQTHFKLSARITNFRQIVRMIRVEVEGNTGPEYLKIGTTRYSISSRGPKTFDLRLSREESLALDHRDITIEVIPRSNQNRVTLKSLRLLGCDRSAMDEIQPRYERQPILTNSNKLVYSILEFATLSGLEWAGNMAKKHLSRKLNHPAVCSVSTRAIVKCHPSVDEELFKIIDGAYLQEWKALIDWTESEGFGEMRLHHVEQLLDRMEAVRTRWPYFVKSLKREFGTVTSFVELMRNEMKRMPLHRCQMMAQAIVKIVFGLLSNGTNEAEQLIHVFLNIFTDQDTYHLANDMRSAVQETISRFENALKEEKKLMVEHENMDKESVLRIKNYGFSPFYGAPRIIAKTPESMLIAKIAETIPIDSEENFKWLEQLISMILEKLTRSNSTVTWQNLSDSPSYNLSRVLASCLAICDPVIIRNHFSRLIHIIKYDVEKIFPMSEKSYSNYSLLRSVELLLFVCLEKRGDESKENQEMLDSIVHDLQAVGIRNLCLKILEKVIPHWKDRGPSTFSRNSAESRKVWLPHVPLVSSSANPPNTSIMNWPSTSEDSYIIACTDLILLIPQHLQELDRRKSVPRDDQWIQKLCQLASLSSGCSAYRQCKKLLLAMCHNDENKYKIMRDKYKMQDLLQQLVKKYLDVSKEVGGHQQLTEIVDVLASITKLALIRPDMWRDVCSTHTTWLLRLACYTTDVVASQVVELLIVAVRDSSVGGQLSIQLADSIVEAENGEFIEKIIKRFLIGRDEQLRWTLHGMLRSVIQLASRQNQCILVKKLYNTIYPLAANLGVQGAQLVDLIATYAPRVFSSTELVAMTQSEISTIEKIRNTLNGDGYQGMYKLMSDLGLGWKSINFDRNPCLVCFTSKGSHDVVKMTSIKSDIRYSANTIIYKLISNYEVSKVTIKLTELKKSKSIKKVSLYYSAKSVESVDLKLHPELWRKCAMVTVAENETVINLSLAVPVVTSSLIVEFEEVVDHRGSSQLHCPRCTVPVRTHSGVCESCGENAFQCAKCRAINYVEKEPFLCQSCGFCKYAQISLFVVCRALPGAQHITCDAERGQCVQEITQLLIKMETTKTKLTGYRAACESLYLRNRPLPPYKLHVENNHTSEFFDANGTMNIEQLPFQSITMPMNNLAVAIRTLHSELCQQTQQLMYLHEELNRYDHASEVSVVFHKPQNISYYSTGQSCFGCLCNQLLHSVALLHSSCDDENALNLILSSDSLIEKLGVLAQTYETLREEVEELLVRLMFDRLDVTTKVEKLIHTGDINLSVMVKSLMYAADPTWQQKLKLLIRLAMDKRDENCCLQALMVLSKYLEATKSVTLDERKKIKLTPNKNITKWLTTDEEWKDCFSVASTSTAPTKSLPSNPYQWITDCLFSQWMSVRSAANQLLVNLSRQQFHEPVALLILCENMSKLSDVPSSVCDQFMCSAHTIIDSSVNTKARLFVQQFHVYLIKRIHEECAKLHEQSVNLLSDNMFGERLRCFVELLSLLLSGSNVENVLLKAGADDLLIFLLHSTIFLKRIMTRRTRATDSSRIALEKLLKRVSCRDGTKLMSVCVESLKLVKDTSTLGIIVGVMMEIMDPQQETEESFLIQIEKDIAQEDFLQGRMTHNPYNSSDPGMGPLMRDIKNKICRDTEMIALMEDDNGMELLVNGNIISLSLSVRDVYDRLWKRSNNGSPMLIVYRMRGLMGDAVETFIENFGVADNSEADDEEDEQLVRMTHCLMECGGIDKLMDLLTTNVDSSSGRFLLCYLRKIFERIVKIPIGRKILVQRRMVERMMSVIRTCCADPTNESKVLIGMELYKVVEFVVSDKHVQDILGGIREDDAMWWFDLFEKRGNEEGSVTELHRKTAQILDQMTMSIGNIVLGNDASEGVLVKMYEKVLKWEQIDSGAPPSGATDHQNRSRITKKDQIMLMTEQLATITSNIISSAHGIRLKQKILDSGVISSTCNYLTKDLPNLYQPTESPEWKVFLARPSLKLILTLLAGLARGHQASQKEIAKTTLKLMHRLEQVASDNSIGTLAENVIEALNE
E3 ubiquitin-protein ligase kcmf-1 C 515 Caenorhabditis Elegans MVTPLTGTHEGVSCDGCAFTAFAGNRYKCLRCSDYDLCFSCFTTKNYGDQQTIADIPIHDESHPMQLILSSVDFDLVYQGDPTRHYDERKIVSFTCPYCNITGLTERQFGTHVLSQHPEAPGYSVICPLCIGNTEMEHIQSKETENLSVHWTEIHLHTMENLFRSTEPITTRPVQRRPMLARRGNRAGVSRTAAQGRPLQDEIGAEMAALLRNMGPDSVEDIRRFTEMMTVPLLPGIRSSQRLMTSTGDRPTVVVESAVTHQDPNVQQVIRPLATIPIYPPTSDESGDETPQPAADSADESEDDNDIQELDDMQPIVEDEALKKDEFWKTLKTRISEEDVDLILETMKSTAKVKEDIDDKMPVWTQRPLKRLANAAQVTTTSDSEGDPGWLPLSFETTPIRSTGCGGYWSDKRFLRPRKMQREQSVASSNAEIMEKAEIALALIRASCLHEPVFTDPTKPDIALKEALQHLRLGEKPAKMMEYQAAEELVNMPERDPITTGEMEVEIPDFTARGY
E3 ubiquitin-protein ligase kcmf-1 D 515 Caenorhabditis Elegans MVTPLTGTHEGVSCDGCAFTAFAGNRYKCLRCSDYDLCFSCFTTKNYGDQQTIADIPIHDESHPMQLILSSVDFDLVYQGDPTRHYDERKIVSFTCPYCNITGLTERQFGTHVLSQHPEAPGYSVICPLCIGNTEMEHIQSKETENLSVHWTEIHLHTMENLFRSTEPITTRPVQRRPMLARRGNRAGVSRTAAQGRPLQDEIGAEMAALLRNMGPDSVEDIRRFTEMMTVPLLPGIRSSQRLMTSTGDRPTVVVESAVTHQDPNVQQVIRPLATIPIYPPTSDESGDETPQPAADSADESEDDNDIQELDDMQPIVEDEALKKDEFWKTLKTRISEEDVDLILETMKSTAKVKEDIDDKMPVWTQRPLKRLANAAQVTTTSDSEGDPGWLPLSFETTPIRSTGCGGYWSDKRFLRPRKMQREQSVASSNAEIMEKAEIALALIRASCLHEPVFTDPTKPDIALKEALQHLRLGEKPAKMMEYQAAEELVNMPERDPITTGEMEVEIPDFTARGY
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2025-01-09
Deposition Author(s): Clausen, T. , Grabarczyk, D.B.