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- EMDB-53433: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term di... -

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Basic information

Entry
Database: EMDB / ID: EMD-53433
TitleCryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term dimer interface focused refinement)
Map data
Sample
  • Complex: C. elegans UBR4/KCMF1 complex
    • Protein or peptide: UBR-type domain-containing protein
    • Protein or peptide: KCMF1
  • Ligand: ZINC ION
KeywordsUbiquitin ligase / protein quality control / LIGASE
Function / homology
Function and homology information


regulation of signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation / synaptic signaling / regulation of cell communication / RING-type E3 ubiquitin transferase / DNA replication / synapse / DNA binding / zinc ion binding ...regulation of signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation / synaptic signaling / regulation of cell communication / RING-type E3 ubiquitin transferase / DNA replication / synapse / DNA binding / zinc ion binding / nucleus / plasma membrane
Similarity search - Function
Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / DNA polymerase processivity factor / DNA polymerase processivity factor / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. ...Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / DNA polymerase processivity factor / DNA polymerase processivity factor / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / : / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile.
Similarity search - Domain/homology
UBR-type domain-containing protein / E3 ubiquitin-protein ligase kcmf-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGrabarczyk DB / Clausen T
Funding support Austria, European Union, 2 items
OrganizationGrant numberCountry
Austrian Research Promotion Agency852936 Austria
H2020 Marie Curie Actions of the European Commission847548European Union
CitationJournal: Science / Year: 2025
Title: Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control.
Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee ...Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee / Jin Seok Shin / Anton Meinhart / Gijs A Versteeg / Eszter Zavodszky / Hyun Kyu Song / Ramanujan S Hegde / Tim Clausen /
Abstract: Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome ...Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome system, where UBR4 acts as an essential E4 ubiquitin ligase, amplifying degradation marks on defective proteins. Cryo-electron microscopy analysis of UBR4 in complex with its cofactors KCMF1 and CALM1 reveals a massive 1.3-megadalton ring structure, featuring a central substrate-binding arena and flexibly attached catalytic units. Our structure shows how UBR4 binds substrate and extends lysine-48-specific ubiquitin chains. Efficient substrate targeting depends on both preubiquitination and specific N-degrons, with KCMF1 acting as a key substrate filter. The architecture of the E4 megacomplex is conserved across eukaryotes, but species-specific adaptations allow UBR4 to perform its precisely tuned quality control function in diverse cellular environments.
History
DepositionApr 15, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53433.png

Downloads & links

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Map

FileDownload / File: emd_53433.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 384 pix.
= 486.912 Å		1.27 Å/pix.
x 384 pix.
= 486.912 Å		1.27 Å/pix.
x 384 pix.
= 486.912 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.03198187 - 0.06431721
Average (Standard dev.)-0.0000730003 (±0.0015700712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 486.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53433_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_53433_half_map_1.map
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Half map: #2

Fileemd_53433_half_map_2.map
Projections & Slices
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Sample components

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Entire : C. elegans UBR4/KCMF1 complex

EntireName: C. elegans UBR4/KCMF1 complex
Components
  • Complex: C. elegans UBR4/KCMF1 complex
    • Protein or peptide: UBR-type domain-containing protein
    • Protein or peptide: KCMF1
  • Ligand: ZINC ION

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Supramolecule #1: C. elegans UBR4/KCMF1 complex

SupramoleculeName: C. elegans UBR4/KCMF1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: UBR-type domain-containing protein

MacromoleculeName: UBR-type domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 488.244844 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDPRETAIGL VRYVTENAAK DFDGESIAAI IYRLRVVENY VSSDVDIICE AMRILIKKLV NLPPITFSPD VWMPIMTSIT EGAIEPQWR IMMESIDISK FSSTSSNFVH MDSITASSTK CSEQITSICK GFALEFGLTR RLFSAIWNTD LEETARKMMN Q EWDSVKID ...String:
MDPRETAIGL VRYVTENAAK DFDGESIAAI IYRLRVVENY VSSDVDIICE AMRILIKKLV NLPPITFSPD VWMPIMTSIT EGAIEPQWR IMMESIDISK FSSTSSNFVH MDSITASSTK CSEQITSICK GFALEFGLTR RLFSAIWNTD LEETARKMMN Q EWDSVKID SSPDSAKQAA GLIEKSIFDL FSEMKDHETF ANELYYAALA RILNNSRRLQ ENKKPAIQDS EDISFYESSL HI YDELIKK LWPHLSKKDP NVKKNTLIIF EKLISLSPTD VLVQRITEKF IDSCEWLKIS GEEICTSMEP RLWKIVGSLV SRI LDLKKT IPYEIVSYAI AVHITQEVTL ASPEVSDCGP DSFDSTCDQP SNMKERFLRH MVDSYFQTRS SLLSIIQFLR TAKS SEEIV QFMRVFYPEL VFGNETLITH AAIEMLRESA SHHSIKADDF ISIVLSVIDA PAIVRIIDVI SCIKDEKVRK EAVEK TIIR MANDLEDEDQ KREGYVNHLH ENGSFWNDIA KYADASILDK AGKRFVEVSV DSMDIRSSVL ATDIFLTILK LKLTSE AER EPESCVICNV SYSNIKIDLE KWNKMGNILV ECNMVKRSKS EALPLFTIHQ LENIDLPMRD LVYVVTQMKF LDTKEGM EL HRKFYDGLPG VNVIFEKFMS KSHKIELCMK LLDEFAKIIA INEKSLIFSL DHENILDWLE EIGVLDSPQI TEKLVDIC F SIEVWDVLTL LQLDGPECHY WDLQMFGRFW KTSLMDLLDE KMMKKVNEKM GSILKEQYDK QSHVAKATRE KRSNGKFPN RPKVADWEEQ LLLMHNRIAG HLTKKKVEDF ADESTQKFTW LLGVCSGQMS YKKEVAVDAE KILSRLYPDA EKRNEVLYHF GVSSILKGL DRPRGKLSLH ILFMQIYLDL VQIDSKSWKI DDSVQKLSRR LGGFNEWLMI VDEEKREDDG GFRIYIVLNL S HYFWELLE GCKASQVVDA HAILKIRKFA EVLASILDKI TFWPNPKLHA YYYIAQFLEP LETIFHFPEI AEQNRKVIES FF KQLFDKL LEQKYQEGLL QDTKLIIQKT DKYLSSSLNL FNEYNTQEPS KIYPVNEIFS LFCRYGSENV HLYCLKMIKK SLQ TLASNI LEHEHILKGE VCIETELQKR LVCDAVLLTE FFGYFSCIYA QVSENQPSEH DDVAKAFMLL DSDIHLKTKS RKRS TQNSV AVGSHRHQTA ENMDLNFCTY KSTGRAYVTQ HWYNCYTCNM MESEGVCSVC AINCHRGHDL AYSKKGSFFC DCGEK KCGA MQGIYHLPNS MYSLRGQLPE KNGDKTLPKI RNVFEHRFEN LNSNCCDELK SALNDVQEEF KEVQDDLEQI LEAVDF ANQ KALQVTEERL AVLESFNDMD DVIISEKEKF IEPLESGHFL PTRRDDLPVQ ELRVASSQHK IRELSDIIKL DDGTELL VL IPESIQTCLQ LHYMDTRTNL IQGMHALRTE TEQIPFNARS LHVSGNRLVV CGQYEFFALR FSPQGDVIDR AHIKLLEN G ASSSMNNNPV VRAKFCREIE SDKRRRQLIA VATMQYIRIY DLTLHETNFV EEMVLPAGNV EDVEIINQED GNVRILVLS SSGYLYEHNI SVFNAENNSI FLTNVVNTPG MDMNGDGVSL HYSSTFNLLF VSLENGAFVA QLPEPTGNST APIYDWKHLN IKNPVDAWK ETSGIIACLS TNCNHQVNYF HPTVGKILLQ KTSVKRSIMT YFLMTSAKNQ SVYSVLIYPN VPTCEIWETS W NNVHDLWI DDVPTERYAV EVVEQKSTQI PIDRDELVLL AEQCEQIRTV DWNCREIGMF YTHEELNNRL SSSDSLPITL IQ QTHFKLS ARITNFRQIV RMIRVEVEGN TGPEYLKIGT TRYSISSRGP KTFDLRLSRE ESLALDHRDI TIEVIPRSNQ NRV TLKSLR LLGCDRSAMD EIQPRYERQP ILTNSNKLVY SILEFATLSG LEWAGNMAKK HLSRKLNHPA VCSVSTRAIV KCHP SVDEE LFKIIDGAYL QEWKALIDWT ESEGFGEMRL HHVEQLLDRM EAVRTRWPYF VKSLKREFGT VTSFVELMRN EMKRM PLHR CQMMAQAIVK IVFGLLSNGT NEAEQLIHVF LNIFTDQDTY HLANDMRSAV QETISRFENA LKEEKKLMVE HENMDK ESV LRIKNYGFSP FYGAPRIIAK TPESMLIAKI AETIPIDSEE NFKWLEQLIS MILEKLTRSN STVTWQNLSD SPSYNLS RV LASCLAICDP VIIRNHFSRL IHIIKYDVEK IFPMSEKSYS NYSLLRSVEL LLFVCLEKRG DESKENQEML DSIVHDLQ A VGIRNLCLKI LEKVIPHWKD RGPSTFSRNS AESRKVWLPH VPLVSSSANP PNTSIMNWPS TSEDSYIIAC TDLILLIPQ HLQELDRRKS VPRDDQWIQK LCQLASLSSG CSAYRQCKKL LLAMCHNDEN KYKIMRDKYK MQDLLQQLVK KYLDVSKEVG GHQQLTEIV DVLASITKLA LIRPDMWRDV CSTHTTWLLR LACYTTDVVA SQVVELLIVA VRDSSVGGQL SIQLADSIVE A ENGEFIEK IIKRFLIGRD EQLRWTLHGM LRSVIQLASR QNQCILVKKL YNTIYPLAAN LGVQGAQLVD LIATYAPRVF SS TELVAMT QSEISTIEKI RNTLNGDGYQ GMYKLMSDLG LGWKSINFDR NPCLVCFTSK GSHDVVKMTS IKSDIRYSAN TII YKLISN YEVSKVTIKL TELKKSKSIK KVSLYYSAKS VESVDLKLHP ELWRKCAMVT VAENETVINL SLAVPVVTSS LIVE FEEVV DHRGSSQLHC PRCTVPVRTH SGVCESCGEN AFQCAKCRAI NYVEKEPFLC QSCGFCKYAQ ISLFVVCRAL PGAQH ITCD AERGQCVQEI TQLLIKMETT KTKLTGYRAA CESLYLRNRP LPPYKLHVEN NHTSEFFDAN GTMNIEQLPF QSITMP MNN LAVAIRTLHS ELCQQTQQLM YLHEELNRYD HASEVSVVFH KPQNISYYST GQSCFGCLCN QLLHSVALLH SSCDDEN AL NLILSSDSLI EKLGVLAQTY ETLREEVEEL LVRLMFDRLD VTTKVEKLIH TGDINLSVMV KSLMYAADPT WQQKLKLL I RLAMDKRDEN CCLQALMVLS KYLEATKSVT LDERKKIKLT PNKNITKWLT TDEEWKDCFS VASTSTAPTK SLPSNPYQW ITDCLFSQWM SVRSAANQLL VNLSRQQFHE PVALLILCEN MSKLSDVPSS VCDQFMCSAH TIIDSSVNTK ARLFVQQFHV YLIKRIHEE CAKLHEQSVN LLSDNMFGER LRCFVELLSL LLSGSNVENV LLKAGADDLL IFLLHSTIFL KRIMTRRTRA T DSSRIALE KLLKRVSCRD GTKLMSVCVE SLKLVKDTST LGIIVGVMME IMDPQQETEE SFLIQIEKDI AQEDFLQGRM TH NPYNSSD PGMGPLMRDI KNKICRDTEM IALMEDDNGM ELLVNGNIIS LSLSVRDVYD RLWKRSNNGS PMLIVYRMRG LMG DAVETF IENFGVADNS EADDEEDEQL VRMTHCLMEC GGIDKLMDLL TTNVDSSSGR FLLCYLRKIF ERIVKIPIGR KILV QRRMV ERMMSVIRTC CADPTNESKV LIGMELYKVV EFVVSDKHVQ DILGGIREDD AMWWFDLFEK RGNEEGSVTE LHRKT AQIL DQMTMSIGNI VLGNDASEGV LVKMYEKVLK WEQIDSGAPP SGATDHQNRS RITKKDQIML MTEQLATITS NIISSA HGI RLKQKILDSG VISSTCNYLT KDLPNLYQPT ESPEWKVFLA RPSLKLILTL LAGLARGHQA SQKEIAKTTL KLMHRLE QV ASDNSIGTLA ENVIEALNED EEVRNQIKLV RDETEKKKKQ MAMLNREKQL TKMRMKVGTG GQIKVSSRTL HNEPSIDD S DSLPCCICRE SVISGDKSAG VYAFAAIDPD SGKTSTVSMM VMVHFNCHKD AIRGGGGRAA DEWTRSKLHN AGAKCNVIT PISMGVVIGD AWIDALHRFE NDVGRVSGLA HGVVNRNFVF VDICNLIDRF IYKRSFSNQS EGGGRESNMQ YLAILHLLGI TLPADAELE ISAPNHRLIA FLFTELTADS WNDQRNDVLR AGINDAQTNG APATWDGFKP TLMTWAFVDA YFNKVIKITG E DRLEWLRE HLVETINKTR GFVDDFDSNI LPCEDVAEFC DVTGAPIDDV NLFLAGGPPQ GSLEVLFQGP AEAAAKEAAA KE AAAKEAA AKALEAEAAA KEAAAKEAAA KEAAAKAHHH HHHHHHH

UniProtKB: UBR-type domain-containing protein

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Macromolecule #2: KCMF1

MacromoleculeName: KCMF1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 62.912762 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVTPLTGTHE GVSCDGCAFT AFAGNRYKCL RCSDYDLCFS CFTTKNYGDQ QTIADIPIHD ESHPMQLILS SVDFDLVYQG DPTRHYDER KIVSFTCPYC NITGLTERQF GTHVLSQHPE APGYSVICPL CIGNTEMEHI QSKETENLSV HWTEIHLHTM E NLFRSTEP ...String:
MVTPLTGTHE GVSCDGCAFT AFAGNRYKCL RCSDYDLCFS CFTTKNYGDQ QTIADIPIHD ESHPMQLILS SVDFDLVYQG DPTRHYDER KIVSFTCPYC NITGLTERQF GTHVLSQHPE APGYSVICPL CIGNTEMEHI QSKETENLSV HWTEIHLHTM E NLFRSTEP ITTRPVQRRP MLARRGNRAG VSRTAAQGRP LQDEIEMMTV PLLPGIRSSQ RLMTSTGDRP TVVVESAVTH QD PNVQQVI RPLATIPIYP PTSDESGDET PQPAADSADE SEDDNDIQEL DDMQPIVEDE ALKKDEFWKT LKTRISEEDV DLI LETMKS TAKVKEDIDD KMPVWTQRPL KRLANAAQVT TTSDSEGDPG WLPLSFETTP IRSTGCGGYW SDKRFLRPRK MQRE QSVAS SNAEIMEKAE IALALIRASC LHEPVFTDPT KPDIALKEAL QHLRLGEKPA KMMEYQAAEE LVNMPERDPI TTGEM EVEI PDFTARGYGQ IVDGNIPLGV VPEADEAITN SEDEEIVGGE TSGDDEDEQE DDENDSQDSS VPEEINIDSA WSHPQF EK

UniProtKB: E3 ubiquitin-protein ligase kcmf-1

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86845
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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