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- PDB-9qx1: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term di... -

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Basic information

Entry
Database: PDB / ID: 9qx1
TitleCryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term dimer interface focused refinement)
Components
  • KCMF1
  • UBR-type domain-containing protein
KeywordsLIGASE / Ubiquitin ligase / protein quality control
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGrabarczyk, D.B. / Clausen, T.
Funding support Austria, European Union, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Sep 17, 2025Group: Data collection / Database references / Category: citation_author / em_admin
Item: _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.3Oct 22, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBR-type domain-containing protein
C: KCMF1
B: UBR-type domain-containing protein
D: KCMF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,102,4466
Polymers1,102,3154
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein UBR-type domain-containing protein


Mass: 488244.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ubr-4, C44E4.1, CELE_C44E4.1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0S4XR36
#2: Protein KCMF1


Mass: 62912.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ZK652.6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34664
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C. elegans UBR4/KCMF1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86845 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315184
ELECTRON MICROSCOPYf_angle_d0.50820570
ELECTRON MICROSCOPYf_dihedral_angle_d3.7332027
ELECTRON MICROSCOPYf_chiral_restr0.0372436
ELECTRON MICROSCOPYf_plane_restr0.0042606

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