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- EMDB-53430: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (N-term f... -

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Basic information

Entry
Database: EMDB / ID: EMD-53430
TitleCryo-EM structure of the human UBR4/KCMF1/CALM1 complex (N-term focused refinement)
Map data
Sample
  • Complex: Human UBR4/KCMF1/CALM1 complex
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4
KeywordsUbiquitin ligase / protein quality control / LIGASE
Function / homology
Function and homology information


negative regulation of HRI-mediated signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / tertiary granule membrane ...negative regulation of HRI-mediated signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / tertiary granule membrane / ficolin-1-rich granule membrane / protein K48-linked ubiquitination / specific granule membrane / positive regulation of autophagy / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / response to oxidative stress / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / calmodulin binding / endosome / protein stabilization / centrosome / Neutrophil degranulation / zinc ion binding / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / 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) ...E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / 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 / Armadillo-type fold / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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_53430.png

Downloads & links

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Map

FileDownload / File: emd_53430.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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: 0.00397
Minimum - Maximum-0.013686591 - 0.02817853
Average (Standard dev.)-0.000067287474 (±0.0007781263)
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_53430_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_53430_half_map_1.map
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Half map: #2

Fileemd_53430_half_map_2.map
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Sample components

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Entire : Human UBR4/KCMF1/CALM1 complex

EntireName: Human UBR4/KCMF1/CALM1 complex
Components
  • Complex: Human UBR4/KCMF1/CALM1 complex
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4

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Supramolecule #1: Human UBR4/KCMF1/CALM1 complex

SupramoleculeName: Human UBR4/KCMF1/CALM1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase UBR4

MacromoleculeName: E3 ubiquitin-protein ligase UBR4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 575.844 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATSGGEEAA AAAPAPGTPA TGADTTPGWE VAVRPLLSAS YSAFEMKELP QLVASVIESE SEILHHEKQY EPFYSSFVAL STHYITTVC SLIPRNQLQS VAAACKVLIE FSLLRLENPD EACAVSQKHL ILLIKGLCTG CSRLDRTEII TFTAMMKSAK L PQTVKTLS ...String:
MATSGGEEAA AAAPAPGTPA TGADTTPGWE VAVRPLLSAS YSAFEMKELP QLVASVIESE SEILHHEKQY EPFYSSFVAL STHYITTVC SLIPRNQLQS VAAACKVLIE FSLLRLENPD EACAVSQKHL ILLIKGLCTG CSRLDRTEII TFTAMMKSAK L PQTVKTLS DVEDQKELAS PVSPELRQKE VQMNFLNQLT SVFNPRTVAS QPISTQTLVE GENDEQSSTD QASAIKTKNV FI AQNVASL QELGGSEKLL RVCLNLPYFL RYINRFQDAV LANSFFIMPA TVADATAVRN GFHSLVIDVT MALDTLSLPV LEP LNPSRL QDVTVLSLSC LYAGVSVATC MAILHVGSAQ QVRTGSTSSK EDDYESDAAT IVQKCLEIYD MIGQAISSSR RAGG EHYQN FQLLGAWCLL NSLFLILNLS PTALADKGKE KDPLAALRVR DILSRTKEGV GSPKLGPGKG HQGFGVLSVI LANHA IKLL TSLFQDLQVE ALHKGWETDG PPAALSIMAQ STSIQRIQRL IDSVPLMNLL LTLLSTSYRK ACVLQRQRKG SMSSDA SAS TDSNTYYEDD FSSTEEDSSQ DDDSEPILGQ WFEETISPSK EKAAPPPPPP PPPLESSPRV KSPSKQAPGE KGNILAS RK DPELFLGLAS NILNFITSSM LNSRNNFIRN YLSVSLSEHH MATLASIIKE VDKDGLKGSS DEEFAAALYH FNHSLVTS D LQSPNLQNTL LQQLGVAPFS EGPWPLYIHP QSLSVLSRLL LIWQHKASAQ GDPDVPECLK VWDRFLSTMK QNALQGVVP SETEDLNVEH LQMLLLIFHN FTETGRRAIL SLFVQIIQEL SVNMDAQMRF VPLILARLLL IFDYLLHQYS KAPVYLFEQV QHNLLSPPF GWASGSQDSN SRRATTPLYH GFKEVEENWS KHFSSDAVPH PRFYCVLSPE ASEDDLNRLD SVACDVLFSK L VKYDELYA ALTALLAAGS QLDTVRRKEN KNVTALEACA LQYYFLILWR ILGILPPSKT YINQLSMNSP EMSECDILHT LR WSSRLRI SSYVNWIKDH LIKQGMKAEH ASSLLELAST TKCSSVKYDV EIVEEYFARQ ISSFCSIDCT TILQLHEIPS LQS IYTLDA AISKVQVSLD EHFSKMAAET DPHKSSEITK NLLPATLQLI DTYASFTRAY LLQNFNEEGT TEKPSKEKLQ GFAA VLAIG SSRCKANTLG PTLVQNLPSS VQTVCESWNN INTNEFPNIG SWRNAFANDT IPSESYISAV QAAHLGTLCS QSLPL AASL KHTLLSLVRL TGDLIVWSDE MNPPQVIRTL LPLLLESSTE SVAEISSNSL ERILGPAESD EFLARVYEKL ITGCYN ILA NHADPNSGLD ESILEECLQY LEKQLESSQA RKAMEEFFSD SGELVQIMMA TANENLSAKF CNRVLKFFTK LFQLTEK SP NPSLLHLCGS LAQLACVEPV RLQAWLTRMT TSPPKDSDQL DVIQENRQLL QLLTTYIVRE NSQVGEGVCA VLLGTLTP M ATEMLANGDG TGFPELMVVM ATLASAGQGA GHLQLHNAAV DWLSRCKKYL SQKNVVEKLN ANVMHGKHVM ILECTCHIM SYLADVTNAL SQSNGQGPSH LSVDGEERAI EVDSDWVEEL AVEEEDSQAE DSDEDSLCNK LCTFTITQKE FMNQHWYHCH TCKMVDGVG VCTVCAKVCH KDHEISYAKY GSFFCDCGAK EDGSCLALVK RTPSSGMSST MKESAFQSEP RISESLVRHA S TSSPADKA KVTISDGKVA DEEKPKKSSL CRTVEGCREE LQNQANFSFA PLVLDMLNFL MDAIQTNFQQ ASAVGSSSRA QQ ALSELHT VEKAVEMTDQ LMVPTLGSQE GAFENVRMNY SGDQGQTIRQ LISAHVLRRV AMCVLSSPHG RRQHLAVSHE KGK ITVLQL SALLKQADSS KRKLTLTRLA SAPVPFTVLS LTGNPCKEDY LAVCGLKDCH VLTFSSSGSV SDHLVLHPQL ATGN FIIKA VWLPGSQTEL AIVTADFVKI YDLCVDALSP TFYFLLPSSK IRDVTFLFNE EGKNIIVIMS SAGYIYTQLM EEASS AQQG PFYVTNVLEI NHEDLKDSNS QVAGGGVSVY YSHVLQMLFF SYCQGKSFAA TISRTTLEVL QLFPINIKSS NGGSKT SPA LCQWSEVMNH PGLVCCVQQT TGVPLVVMVK PDTFLIQEIK TLPAKAKIQD MVAIRHTACN EQQRTTMILL CEDGSLR IY MANVENTSYW LQPSLQPSSV ISIMKPVRKR KTATITTRTS SQVTFPIDFF EHNQQLTDVE FGGNDLLQVY NAQQIKHR L NSTGMYVANT KPGGFTIEIS NNNSTMVMTG MRIQIGTQAI ERAPSYIEIF GRTMQLNLSR SRWFDFPFTR EEALQADKK LNLFIGASVD PAGVTMIDAV KIYGKTKEQF GWPDEPPEEF PSASVSNICP SNLNQSNGTG DSDSAAPTTT SGTVLERLVV SSLEALESC FAVGPIIEKE RNKNAAQELA TLLLSLPAPA SVQQQSKSLL ASLHTSRSAY HSHKDQALLS KAVQCLNTSS K EGKDLDPE VFQRLVITAR SIAIMRPNNL VHFTESKLPQ METEGMDEGK EPQKQLEGDC CSFITQLVNH FWKLHASKPK NA FLAPACL PGLTHIEATV NALVDIIHGY CTCELDCINT ASKIYMQMLL CPDPAVSFSC KQALIRVLRP RNKRRHVTLP SSP RSNTPM GDKDDDDDDD ADEKMQSSGI PNGGHIRQES QEQSEVDHGD FEMVSESMVL ETAENVNNGN PSPLEALLAG AEGF PPMLD IPPDADDETM VELAIALSLQ QDQQGSSSSA LGLQSLGLSG QAPSSSSLDA GTLSDTTASA PASDDEGSTA ATDGS TLRT SPADHGGSVG SESGGSAVDS VAGEHSVSGR SSAYGDATAE GHPAGPGSVS SSTGAISTTT GHQEGDGSEG EGEGET EGD VHTSNRLHMV RLMLLERLLQ TLPQLRNVGG VRAIPYMQVI LMLTTDLDGE DEKDKGALDN LLSQLIAELG MDKKDVS KK NERSALNEVH LVVMRLLSVF MSRTKSGSKS SICESSSLIS SATAAALLSS GAVDYCLHVL KSLLEYWKSQ QNDEEPVA T SQLLKPHTTS SPPDMSPFFL RQYVKGHAAD VFEAYTQLLT EMVLRLPYQI KKITDTNSRI PPPVFDHSWF YFLSEYLMI QQTPFVRRQV RKLLLFICGS KEKYRQLRDL HTLDSHVRGI KKLLEEQGIF LRASVVTASS GSALQYDTLI SLMEHLKACA EIAAQRTIN WQKFCIKDDS VLYFLLQVSF LVDEGVSPVL LQLLSCALCG SKVLAALAAS SGSSSASSSS APVAASSGQA T TQSKSSTK KSKKEEKEKE KDGETSGSQE DQLCTALVNQ LNKFADKETL IQFLRCFLLE SNSSSVRWQA HCLTLHIYRN SS KSQQELL LDLMWSIWPE LPAYGRKAAQ FVDLLGYFSL KTPQTEKKLK EYSQKAVEIL RTQNHILTNH PNSNIYNTLS GLV EFDGYY LESDPCLVCN NPEVPFCYIK LSSIKVDTRY TTTQQVVKLI GSHTISKVTV KIGDLKRTKM VRTINLYYNN RTVQ AIVEL KNKPARWHKA KKVQLTPGQT EVKIDLPLPI VASNLMIEFA DFYENYQAST ETLQCPRCSA SVPANPGVCG NCGEN VYQC HKCRSINYDE KDPFLCNACG FCKYARFDFM LYAKPCCAVD PIENEEDRKK AVSNINTLLD KADRVYHQLM GHRPQL ENL LCKVNEAAPE KPQDDSGTAG GISSTSASVN RYILQLAQEY CGDCKNSFDE LSKIIQKVFA SRKELLEYDL QQREAAT KS SRTSVQPTFT ASQYRALSVL GCGHTSSTKC YGCASAVTEH CITLLRALAT NPALRHILVS QGLIRELFDY NLRRGAAA M REEVRQLMCL LTRDNPEATQ QMNDLIIGKV STALKGHWAN PDLASSLQYE MLLLTDSISK EDSCWELRLR CALSLFLMA VNIKTPVVVE NITLMCLRIL QKLIKPPAPT SKKNKDVPVE ALTTVKPYCN EIHAQAQLWL KRDPKASYDA WKKCLPIRGI DGNGKAPSK SELRHLYLTE KYVWRWKQFL SRRGKRTSPL DLKLGHNNWL RQVLFTPATQ AARQAACTIV EALATIPSRK Q QVLDLLTS YLDELSIAGE CAAEYLALYQ KLITSAHWKV YLAARGVLPY VGNLITKEIA RLLALEEATL STDLQQGYAL KS LTGLLSS FVEVESIKRH FKSRLVGTVL NGYLCLRKLV VQRTKLIDET QDMLLEMLED MTTGTESETK AFMAVCIETA KRY NLDDYR TPVFIFERLC SIIYPEENEV TEFFVTLEKD PQQEDFLQGR MPGNPYSSNE PGIGPLMRDI KNKICQDCDL VALL EDDSG MELLVNNKII SLDLPVAEVY KKVWCTTNEG EPMRIVYRMR GLLGDATEEF IESLDSTTDE EEDEEEVYKM AGVMA QCGG LECMLNRLAG IRDFKQGRHL LTVLLKLFSY CVKVKVNRQQ LVKLEMNTLN VMLGTLNLAL VAEQESKDSG GAAVAE QVL SIMEIILDES NAEPLSEDKG NLLLTGDKDQ LVMLLDQINS TFVRSNPSVL QGLLRIIPYL SFGEVEKMQI LVERFKP YC NFDKYDEDHS GDDKVFLDCF CKIAAGIKNN SNGHQLKDLI LQKGITQNAL DYMKKHIPSA KNLDADIWKK FLSRPALP F ILRLLRGLAI QHPGTQVLIG TDSIPNLHKL EQVSSDEGIG TLAENLLEAL REHPDVNKKI DAARRETRAE KKRMAMAMR QKALGTLGMT TNEKGQVVTK TALLKQMEEL IEEPGLTCCI CREGYKFQPT KVLGIYTFTK RVALEEMENK PRKQQGYSTV SHFNIVHYD CHLAAVRLAR GREEWESAAL QNANTKCNGL LPVWGPHVPE SAFATCLARH NTYLQECTGQ REPTYQLNIH D IKLLFLRF AMEQSFSADT GGGGRESNIH LIPYIIHTVL YVLNTTRATS REEKNLQGFL EQPKEKWVES AFEVDGPYYF TV LALHILP PEQWRATRVE ILRRLLVTSQ ARAVAPGGAT RLTDKAVKDY SAYRSSLLFW ALVDLIYNMF KKVPTSNTEG GWS CSLAEY IRHNDMPIYE AADKALKTFQ EEFMPVETFS EFLDVAGLLS EITDPESFLK DLLNSVPHHH HHHHHHH

UniProtKB: E3 ubiquitin-protein ligase UBR4

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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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75153
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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