Cryo-em structure of the c. elegans ubr4/kcmf1 complex (n-term focused refinement)
PDB DOI: 10.2210/pdb9qx2/pdb
Classification: LIGASE Organism(s): Caenorhabditis Elegans
Deposited: 2025-04-15 Deposition Author(s): Clausen, T. , Grabarczyk, D.B.
Method: ELECTRON MICROSCOPY Resolution: 5.7 Å
Cryo-em structure of the c. elegans ubr4/kcmf1 complex (n-term focused refinement)
Clausen, T. , Grabarczyk, D.B.
Primary Citation of Related Structures: 9QX2
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 |
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-04-15 Deposition Author(s): Clausen, T. , Grabarczyk, D.B.