Cryo-em structure of the c. elegans ubr4/kcmf1 complex (c-term dimer interface focused refinement)
PDB DOI: 10.2210/pdb9qx1/pdb
Classification: LIGASE Organism(s): Caenorhabditis Elegans
Deposited: 2025-04-15 Deposition Author(s): Clausen, T. , Grabarczyk, D.B.
Method: ELECTRON MICROSCOPY Resolution: 2.6 Å
Cryo-em structure of the c. elegans ubr4/kcmf1 complex (c-term dimer interface focused refinement)
Clausen, T. , Grabarczyk, D.B.
Primary Citation of Related Structures: 9QX1
Proteins | ||||
---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Sequence |
UBR-type domain-containing protein | A | 4284 | Caenorhabditis Elegans | MDPRETAIGLVRYVTENAAKDFDGESIAAIIYRLRVVENYVSSDVDIICEAMRILIKKLVNLPPITFSPDVWMPIMTSITEGAIEPQWRIMMESIDISKFSSTSSNFVHMDSITASSTKCSEQITSICKGFALEFGLTRRLFSAIWNTDLEETARKMMNQEWDSVKIDSSPDSAKQAAGLIEKSIFDLFSEMKDHETFANELYYAALARILNNSRRLQENKKPAIQDSEDISFYESSLHIYDELIKKLWPHLSKKDPNVKKNTLIIFEKLISLSPTDVLVQRITEKFIDSCEWLKISGEEICTSMEPRLWKIVGSLVSRILDLKKTIPYEIVSYAIAVHITQEVTLASPEVSDCGPDSFDSTCDQPSNMKERFLRHMVDSYFQTRSSLLSIIQFLRTAKSSEEIVQFMRVFYPELVFGNETLITHAAIEMLRESASHHSIKADDFISIVLSVIDAPAIVRIIDVISCIKDEKVRKEAVEKTIIRMANDLEDEDQKREGYVNHLHENGSFWNDIAKYADASILDKAGKRFVEVSVDSMDIRSSVLATDIFLTILKLKLTSEAEREPESCVICNVSYSNIKIDLEKWNKMGNILVECNMVKRSKSEALPLFTIHQLENIDLPMRDLVYVVTQMKFLDTKEGMELHRKFYDGLPGVNVIFEKFMSKSHKIELCMKLLDEFAKIIAINEKSLIFSLDHENILDWLEEIGVLDSPQITEKLVDICFSIEVWDVLTLLQLDGPECHYWDLQMFGRFWKTSLMDLLDEKMMKKVNEKMGSILKEQYDKQSHVAKATREKRSNGKFPNRPKVADWEEQLLLMHNRIAGHLTKKKVEDFADESTQKFTWLLGVCSGQMSYKKEVAVDAEKILSRLYPDAEKRNEVLYHFGVSSILKGLDRPRGKLSLHILFMQIYLDLVQIDSKSWKIDDSVQKLSRRLGGFNEWLMIVDEEKREDDGGFRIYIVLNLSHYFWELLEGCKASQVVDAHAILKIRKFAEVLASILDKITFWPNPKLHAYYYIAQFLEPLETIFHFPEIAEQNRKVIESFFKQLFDKLLEQKYQEGLLQDTKLIIQKTDKYLSSSLNLFNEYNTQEPSKIYPVNEIFSLFCRYGSENVHLYCLKMIKKSLQTLASNILEHEHILKGEVCIETELQKRLVCDAVLLTEFFGYFSCIYAQVSENQPSEHDDVAKAFMLLDSDIHLKTKSRKRSTQNSVAVGSHRHQTAENMDLNFCTYKSTGRAYVTQHWYNCYTCNMMESEGVCSVCAINCHRGHDLAYSKKGSFFCDCGEKKCGAMQGIYHLPNSMYSLRGQLPEKNGDKTLPKIRNVFEHRFENLNSNCCDELKSALNDVQEEFKEVQDDLEQILEAVDFANQKALQVTEERLAVLESFNDMDDVIISEKEKFIEPLESGHFLPTRRDDLPVQELRVASSQHKIRELSDIIKLDDGTELLVLIPESIQTCLQLHYMDTRTNLIQGMHALRTETEQIPFNARSLHVSGNRLVVCGQYEFFALRFSPQGDVIDRAHIKLLENGASSSMNNNPVVRAKFCREIESDKRRRQLIAVATMQYIRIYDLTLHETNFVEEMVLPAGNVEDVEIINQEDGNVRILVLSSSGYLYEHNISVFNAENNSIFLTNVVNTPGMDMNGDGVSLHYSSTFNLLFVSLENGAFVAQLPEPTGNSTAPIYDWKHLNIKNPVDAWKETSGIIACLSTNCNHQVNYFHPTVGKILLQKTSVKRSIMTYFLMTSAKNQSVYSVLIYPNVPTCEIWETSWNNVHDLWIDDVPTERYAVEVVEQKSTQIPIDRDELVLLAEQCEQIRTVDWNCREIGMFYTHEELNNRLSSSDSLPITLIQQTHFKLSARITNFRQIVRMIRVEVEGNTGPEYLKIGTTRYSISSRGPKTFDLRLSREESLALDHRDITIEVIPRSNQNRVTLKSLRLLGCDRSAMDEIQPRYERQPILTNSNKLVYSILEFATLSGLEWAGNMAKKHLSRKLNHPAVCSVSTRAIVKCHPSVDEELFKIIDGAYLQEWKALIDWTESEGFGEMRLHHVEQLLDRMEAVRTRWPYFVKSLKREFGTVTSFVELMRNEMKRMPLHRCQMMAQAIVKIVFGLLSNGTNEAEQLIHVFLNIFTDQDTYHLANDMRSAVQETISRFENALKEEKKLMVEHENMDKESVLRIKNYGFSPFYGAPRIIAKTPESMLIAKIAETIPIDSEENFKWLEQLISMILEKLTRSNSTVTWQNLSDSPSYNLSRVLASCLAICDPVIIRNHFSRLIHIIKYDVEKIFPMSEKSYSNYSLLRSVELLLFVCLEKRGDESKENQEMLDSIVHDLQAVGIRNLCLKILEKVIPHWKDRGPSTFSRNSAESRKVWLPHVPLVSSSANPPNTSIMNWPSTSEDSYIIACTDLILLIPQHLQELDRRKSVPRDDQWIQKLCQLASLSSGCSAYRQCKKLLLAMCHNDENKYKIMRDKYKMQDLLQQLVKKYLDVSKEVGGHQQLTEIVDVLASITKLALIRPDMWRDVCSTHTTWLLRLACYTTDVVASQVVELLIVAVRDSSVGGQLSIQLADSIVEAENGEFIEKIIKRFLIGRDEQLRWTLHGMLRSVIQLASRQNQCILVKKLYNTIYPLAANLGVQGAQLVDLIATYAPRVFSSTELVAMTQSEISTIEKIRNTLNGDGYQGMYKLMSDLGLGWKSINFDRNPCLVCFTSKGSHDVVKMTSIKSDIRYSANTIIYKLISNYEVSKVTIKLTELKKSKSIKKVSLYYSAKSVESVDLKLHPELWRKCAMVTVAENETVINLSLAVPVVTSSLIVEFEEVVDHRGSSQLHCPRCTVPVRTHSGVCESCGENAFQCAKCRAINYVEKEPFLCQSCGFCKYAQISLFVVCRALPGAQHITCDAERGQCVQEITQLLIKMETTKTKLTGYRAACESLYLRNRPLPPYKLHVENNHTSEFFDANGTMNIEQLPFQSITMPMNNLAVAIRTLHSELCQQTQQLMYLHEELNRYDHASEVSVVFHKPQNISYYSTGQSCFGCLCNQLLHSVALLHSSCDDENALNLILSSDSLIEKLGVLAQTYETLREEVEELLVRLMFDRLDVTTKVEKLIHTGDINLSVMVKSLMYAADPTWQQKLKLLIRLAMDKRDENCCLQALMVLSKYLEATKSVTLDERKKIKLTPNKNITKWLTTDEEWKDCFSVASTSTAPTKSLPSNPYQWITDCLFSQWMSVRSAANQLLVNLSRQQFHEPVALLILCENMSKLSDVPSSVCDQFMCSAHTIIDSSVNTKARLFVQQFHVYLIKRIHEECAKLHEQSVNLLSDNMFGERLRCFVELLSLLLSGSNVENVLLKAGADDLLIFLLHSTIFLKRIMTRRTRATDSSRIALEKLLKRVSCRDGTKLMSVCVESLKLVKDTSTLGIIVGVMMEIMDPQQETEESFLIQIEKDIAQEDFLQGRMTHNPYNSSDPGMGPLMRDIKNKICRDTEMIALMEDDNGMELLVNGNIISLSLSVRDVYDRLWKRSNNGSPMLIVYRMRGLMGDAVETFIENFGVADNSEADDEEDEQLVRMTHCLMECGGIDKLMDLLTTNVDSSSGRFLLCYLRKIFERIVKIPIGRKILVQRRMVERMMSVIRTCCADPTNESKVLIGMELYKVVEFVVSDKHVQDILGGIREDDAMWWFDLFEKRGNEEGSVTELHRKTAQILDQMTMSIGNIVLGNDASEGVLVKMYEKVLKWEQIDSGAPPSGATDHQNRSRITKKDQIMLMTEQLATITSNIISSAHGIRLKQKILDSGVISSTCNYLTKDLPNLYQPTESPEWKVFLARPSLKLILTLLAGLARGHQASQKEIAKTTLKLMHRLEQVASDNSIGTLAENVIEALNEDEEVRNQIKLVRDETEKKKKQMAMLNREKQLTKMRMKVGTGGQIKVSSRTLHNEPSIDDSDSLPCCICRESVISGDKSAGVYAFAAIDPDSGKTSTVSMMVMVHFNCHKDAIRGGGGRAADEWTRSKLHNAGAKCNVITPISMGVVIGDAWIDALHRFENDVGRVSGLAHGVVNRNFVFVDICNLIDRFIYKRSFSNQSEGGGRESNMQYLAILHLLGITLPADAELEISAPNHRLIAFLFTELTADSWNDQRNDVLRAGINDAQTNGAPATWDGFKPTLMTWAFVDAYFNKVIKITGEDRLEWLREHLVETINKTRGFVDDFDSNILPCEDVAEFCDVTGAPIDDVNLFLAGGPPQGSLEVLFQGPAEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKAHHHHHHHHHH |
UBR-type domain-containing protein | B | 4284 | Caenorhabditis Elegans | MDPRETAIGLVRYVTENAAKDFDGESIAAIIYRLRVVENYVSSDVDIICEAMRILIKKLVNLPPITFSPDVWMPIMTSITEGAIEPQWRIMMESIDISKFSSTSSNFVHMDSITASSTKCSEQITSICKGFALEFGLTRRLFSAIWNTDLEETARKMMNQEWDSVKIDSSPDSAKQAAGLIEKSIFDLFSEMKDHETFANELYYAALARILNNSRRLQENKKPAIQDSEDISFYESSLHIYDELIKKLWPHLSKKDPNVKKNTLIIFEKLISLSPTDVLVQRITEKFIDSCEWLKISGEEICTSMEPRLWKIVGSLVSRILDLKKTIPYEIVSYAIAVHITQEVTLASPEVSDCGPDSFDSTCDQPSNMKERFLRHMVDSYFQTRSSLLSIIQFLRTAKSSEEIVQFMRVFYPELVFGNETLITHAAIEMLRESASHHSIKADDFISIVLSVIDAPAIVRIIDVISCIKDEKVRKEAVEKTIIRMANDLEDEDQKREGYVNHLHENGSFWNDIAKYADASILDKAGKRFVEVSVDSMDIRSSVLATDIFLTILKLKLTSEAEREPESCVICNVSYSNIKIDLEKWNKMGNILVECNMVKRSKSEALPLFTIHQLENIDLPMRDLVYVVTQMKFLDTKEGMELHRKFYDGLPGVNVIFEKFMSKSHKIELCMKLLDEFAKIIAINEKSLIFSLDHENILDWLEEIGVLDSPQITEKLVDICFSIEVWDVLTLLQLDGPECHYWDLQMFGRFWKTSLMDLLDEKMMKKVNEKMGSILKEQYDKQSHVAKATREKRSNGKFPNRPKVADWEEQLLLMHNRIAGHLTKKKVEDFADESTQKFTWLLGVCSGQMSYKKEVAVDAEKILSRLYPDAEKRNEVLYHFGVSSILKGLDRPRGKLSLHILFMQIYLDLVQIDSKSWKIDDSVQKLSRRLGGFNEWLMIVDEEKREDDGGFRIYIVLNLSHYFWELLEGCKASQVVDAHAILKIRKFAEVLASILDKITFWPNPKLHAYYYIAQFLEPLETIFHFPEIAEQNRKVIESFFKQLFDKLLEQKYQEGLLQDTKLIIQKTDKYLSSSLNLFNEYNTQEPSKIYPVNEIFSLFCRYGSENVHLYCLKMIKKSLQTLASNILEHEHILKGEVCIETELQKRLVCDAVLLTEFFGYFSCIYAQVSENQPSEHDDVAKAFMLLDSDIHLKTKSRKRSTQNSVAVGSHRHQTAENMDLNFCTYKSTGRAYVTQHWYNCYTCNMMESEGVCSVCAINCHRGHDLAYSKKGSFFCDCGEKKCGAMQGIYHLPNSMYSLRGQLPEKNGDKTLPKIRNVFEHRFENLNSNCCDELKSALNDVQEEFKEVQDDLEQILEAVDFANQKALQVTEERLAVLESFNDMDDVIISEKEKFIEPLESGHFLPTRRDDLPVQELRVASSQHKIRELSDIIKLDDGTELLVLIPESIQTCLQLHYMDTRTNLIQGMHALRTETEQIPFNARSLHVSGNRLVVCGQYEFFALRFSPQGDVIDRAHIKLLENGASSSMNNNPVVRAKFCREIESDKRRRQLIAVATMQYIRIYDLTLHETNFVEEMVLPAGNVEDVEIINQEDGNVRILVLSSSGYLYEHNISVFNAENNSIFLTNVVNTPGMDMNGDGVSLHYSSTFNLLFVSLENGAFVAQLPEPTGNSTAPIYDWKHLNIKNPVDAWKETSGIIACLSTNCNHQVNYFHPTVGKILLQKTSVKRSIMTYFLMTSAKNQSVYSVLIYPNVPTCEIWETSWNNVHDLWIDDVPTERYAVEVVEQKSTQIPIDRDELVLLAEQCEQIRTVDWNCREIGMFYTHEELNNRLSSSDSLPITLIQQTHFKLSARITNFRQIVRMIRVEVEGNTGPEYLKIGTTRYSISSRGPKTFDLRLSREESLALDHRDITIEVIPRSNQNRVTLKSLRLLGCDRSAMDEIQPRYERQPILTNSNKLVYSILEFATLSGLEWAGNMAKKHLSRKLNHPAVCSVSTRAIVKCHPSVDEELFKIIDGAYLQEWKALIDWTESEGFGEMRLHHVEQLLDRMEAVRTRWPYFVKSLKREFGTVTSFVELMRNEMKRMPLHRCQMMAQAIVKIVFGLLSNGTNEAEQLIHVFLNIFTDQDTYHLANDMRSAVQETISRFENALKEEKKLMVEHENMDKESVLRIKNYGFSPFYGAPRIIAKTPESMLIAKIAETIPIDSEENFKWLEQLISMILEKLTRSNSTVTWQNLSDSPSYNLSRVLASCLAICDPVIIRNHFSRLIHIIKYDVEKIFPMSEKSYSNYSLLRSVELLLFVCLEKRGDESKENQEMLDSIVHDLQAVGIRNLCLKILEKVIPHWKDRGPSTFSRNSAESRKVWLPHVPLVSSSANPPNTSIMNWPSTSEDSYIIACTDLILLIPQHLQELDRRKSVPRDDQWIQKLCQLASLSSGCSAYRQCKKLLLAMCHNDENKYKIMRDKYKMQDLLQQLVKKYLDVSKEVGGHQQLTEIVDVLASITKLALIRPDMWRDVCSTHTTWLLRLACYTTDVVASQVVELLIVAVRDSSVGGQLSIQLADSIVEAENGEFIEKIIKRFLIGRDEQLRWTLHGMLRSVIQLASRQNQCILVKKLYNTIYPLAANLGVQGAQLVDLIATYAPRVFSSTELVAMTQSEISTIEKIRNTLNGDGYQGMYKLMSDLGLGWKSINFDRNPCLVCFTSKGSHDVVKMTSIKSDIRYSANTIIYKLISNYEVSKVTIKLTELKKSKSIKKVSLYYSAKSVESVDLKLHPELWRKCAMVTVAENETVINLSLAVPVVTSSLIVEFEEVVDHRGSSQLHCPRCTVPVRTHSGVCESCGENAFQCAKCRAINYVEKEPFLCQSCGFCKYAQISLFVVCRALPGAQHITCDAERGQCVQEITQLLIKMETTKTKLTGYRAACESLYLRNRPLPPYKLHVENNHTSEFFDANGTMNIEQLPFQSITMPMNNLAVAIRTLHSELCQQTQQLMYLHEELNRYDHASEVSVVFHKPQNISYYSTGQSCFGCLCNQLLHSVALLHSSCDDENALNLILSSDSLIEKLGVLAQTYETLREEVEELLVRLMFDRLDVTTKVEKLIHTGDINLSVMVKSLMYAADPTWQQKLKLLIRLAMDKRDENCCLQALMVLSKYLEATKSVTLDERKKIKLTPNKNITKWLTTDEEWKDCFSVASTSTAPTKSLPSNPYQWITDCLFSQWMSVRSAANQLLVNLSRQQFHEPVALLILCENMSKLSDVPSSVCDQFMCSAHTIIDSSVNTKARLFVQQFHVYLIKRIHEECAKLHEQSVNLLSDNMFGERLRCFVELLSLLLSGSNVENVLLKAGADDLLIFLLHSTIFLKRIMTRRTRATDSSRIALEKLLKRVSCRDGTKLMSVCVESLKLVKDTSTLGIIVGVMMEIMDPQQETEESFLIQIEKDIAQEDFLQGRMTHNPYNSSDPGMGPLMRDIKNKICRDTEMIALMEDDNGMELLVNGNIISLSLSVRDVYDRLWKRSNNGSPMLIVYRMRGLMGDAVETFIENFGVADNSEADDEEDEQLVRMTHCLMECGGIDKLMDLLTTNVDSSSGRFLLCYLRKIFERIVKIPIGRKILVQRRMVERMMSVIRTCCADPTNESKVLIGMELYKVVEFVVSDKHVQDILGGIREDDAMWWFDLFEKRGNEEGSVTELHRKTAQILDQMTMSIGNIVLGNDASEGVLVKMYEKVLKWEQIDSGAPPSGATDHQNRSRITKKDQIMLMTEQLATITSNIISSAHGIRLKQKILDSGVISSTCNYLTKDLPNLYQPTESPEWKVFLARPSLKLILTLLAGLARGHQASQKEIAKTTLKLMHRLEQVASDNSIGTLAENVIEALNEDEEVRNQIKLVRDETEKKKKQMAMLNREKQLTKMRMKVGTGGQIKVSSRTLHNEPSIDDSDSLPCCICRESVISGDKSAGVYAFAAIDPDSGKTSTVSMMVMVHFNCHKDAIRGGGGRAADEWTRSKLHNAGAKCNVITPISMGVVIGDAWIDALHRFENDVGRVSGLAHGVVNRNFVFVDICNLIDRFIYKRSFSNQSEGGGRESNMQYLAILHLLGITLPADAELEISAPNHRLIAFLFTELTADSWNDQRNDVLRAGINDAQTNGAPATWDGFKPTLMTWAFVDAYFNKVIKITGEDRLEWLREHLVETINKTRGFVDDFDSNILPCEDVAEFCDVTGAPIDDVNLFLAGGPPQGSLEVLFQGPAEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKAHHHHHHHHHH |
KCMF1 | C | 562 | Caenorhabditis Elegans | MVTPLTGTHEGVSCDGCAFTAFAGNRYKCLRCSDYDLCFSCFTTKNYGDQQTIADIPIHDESHPMQLILSSVDFDLVYQGDPTRHYDERKIVSFTCPYCNITGLTERQFGTHVLSQHPEAPGYSVICPLCIGNTEMEHIQSKETENLSVHWTEIHLHTMENLFRSTEPITTRPVQRRPMLARRGNRAGVSRTAAQGRPLQDEIEMMTVPLLPGIRSSQRLMTSTGDRPTVVVESAVTHQDPNVQQVIRPLATIPIYPPTSDESGDETPQPAADSADESEDDNDIQELDDMQPIVEDEALKKDEFWKTLKTRISEEDVDLILETMKSTAKVKEDIDDKMPVWTQRPLKRLANAAQVTTTSDSEGDPGWLPLSFETTPIRSTGCGGYWSDKRFLRPRKMQREQSVASSNAEIMEKAEIALALIRASCLHEPVFTDPTKPDIALKEALQHLRLGEKPAKMMEYQAAEELVNMPERDPITTGEMEVEIPDFTARGYGQIVDGNIPLGVVPEADEAITNSEDEEIVGGETSGDDEDEQEDDENDSQDSSVPEEINIDSAWSHPQFEK |
KCMF1 | D | 562 | Caenorhabditis Elegans | MVTPLTGTHEGVSCDGCAFTAFAGNRYKCLRCSDYDLCFSCFTTKNYGDQQTIADIPIHDESHPMQLILSSVDFDLVYQGDPTRHYDERKIVSFTCPYCNITGLTERQFGTHVLSQHPEAPGYSVICPLCIGNTEMEHIQSKETENLSVHWTEIHLHTMENLFRSTEPITTRPVQRRPMLARRGNRAGVSRTAAQGRPLQDEIEMMTVPLLPGIRSSQRLMTSTGDRPTVVVESAVTHQDPNVQQVIRPLATIPIYPPTSDESGDETPQPAADSADESEDDNDIQELDDMQPIVEDEALKKDEFWKTLKTRISEEDVDLILETMKSTAKVKEDIDDKMPVWTQRPLKRLANAAQVTTTSDSEGDPGWLPLSFETTPIRSTGCGGYWSDKRFLRPRKMQREQSVASSNAEIMEKAEIALALIRASCLHEPVFTDPTKPDIALKEALQHLRLGEKPAKMMEYQAAEELVNMPERDPITTGEMEVEIPDFTARGYGQIVDGNIPLGVVPEADEAITNSEDEEIVGGETSGDDEDEQEDDENDSQDSSVPEEINIDSAWSHPQFEK |
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-04-15 Deposition Author(s): Clausen, T. , Grabarczyk, D.B.