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- EMDB-52502: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map) -

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Basic information

Entry
Database: EMDB / ID: EMD-52502
TitleCryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map)
Map data
Sample
  • Complex: UBR4/KCMF1 ubiquitin ligase complex
    • Protein or peptide: UBR-type domain-containing protein
    • Protein or peptide: E3 ubiquitin-protein ligase kcmf-1
  • Ligand: ZINC ION
KeywordsUbiquitin ligase Protein quality control / LIGASE
Function / homology
Function and homology information


Antigen processing: Ubiquitination & Proteasome degradation / regulation of signaling / Neutrophil degranulation / synaptic signaling / regulation of cell communication / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / late endosome / DNA replication / lysosome ...Antigen processing: Ubiquitination & Proteasome degradation / regulation of signaling / Neutrophil degranulation / synaptic signaling / regulation of cell communication / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / late endosome / DNA replication / lysosome / synapse / DNA binding / zinc ion binding / plasma membrane
Similarity search - Function
Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / 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. / DNA polymerase processivity factor / DNA polymerase processivity factor ...Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / 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. / DNA polymerase processivity factor / DNA polymerase processivity factor / : / 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 finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / 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: 3.0 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: To Be Published
Title: Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control
Authors: 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
History
DepositionJan 9, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52502.png

Downloads & links

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Map

FileDownload / File: emd_52502.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0104
Minimum - Maximum0.0 - 0.05380428
Average (Standard dev.)0.009822927 (±0.00064411643)
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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Sample components

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Entire : UBR4/KCMF1 ubiquitin ligase complex

EntireName: UBR4/KCMF1 ubiquitin ligase complex
Components
  • Complex: UBR4/KCMF1 ubiquitin ligase complex
    • Protein or peptide: UBR-type domain-containing protein
    • Protein or peptide: E3 ubiquitin-protein ligase kcmf-1
  • Ligand: ZINC ION

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Supramolecule #1: UBR4/KCMF1 ubiquitin ligase complex

SupramoleculeName: UBR4/KCMF1 ubiquitin ligase 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: 441.954656 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 ENVIEALNE

UniProtKB: UBR-type domain-containing protein

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Macromolecule #2: E3 ubiquitin-protein ligase kcmf-1

MacromoleculeName: E3 ubiquitin-protein ligase kcmf-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 57.890016 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 LQDEIGAEMA ALLRNMGPDS VEDIRRFTEM MTVPLLPGIR SS QRLMTST GDRPTVVVES AVTHQDPNVQ QVIRPLATIP IYPPTSDESG DETPQPAADS ADESEDDNDI QELDDMQPIV EDE ALKKDE FWKTLKTRIS EEDVDLILET MKSTAKVKED IDDKMPVWTQ RPLKRLANAA QVTTTSDSEG DPGWLPLSFE TTPI RSTGC GGYWSDKRFL RPRKMQREQS VASSNAEIME KAEIALALIR ASCLHEPVFT DPTKPDIALK EALQHLRLGE KPAKM MEYQ AAEELVNMPE RDPITTGEME VEIPDFTARG Y

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: 18 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 691759
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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