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- PDB-9hyf: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map) -

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Basic information

Entry
Database: PDB / ID: 9hyf
TitleCryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map)
Components
  • E3 ubiquitin-protein ligase kcmf-1
  • UBR-type domain-containing protein
KeywordsLIGASE / Ubiquitin ligase Protein quality control
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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: To Be Published
Title: Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control
Authors: Grabarczyk, D.B. / Ehrmann, J.F. / Murphy, P. / Kurzbauer, R. / Bell, L.E. / Deszcz, L. / Neuhold, J. / Schleiffer, A. / Shulkina, A. / Versteeg, G.A. / Meinhart, A. / Zavodszky, E. / Hegde, R.S. / Clausen, T.
History
DepositionJan 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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: E3 ubiquitin-protein ligase kcmf-1
B: UBR-type domain-containing protein
D: E3 ubiquitin-protein ligase kcmf-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,000,86722
Polymers999,6894
Non-polymers1,17718
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: 441954.656 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 E3 ubiquitin-protein ligase kcmf-1 / KCMF1 homolog / Potassium channel modulatory factor kcmf-1


Mass: 57890.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: kcmf-1, ZK652.6 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P34664, RING-type E3 ubiquitin transferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / 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: UBR4/KCMF1 ubiquitin ligase 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 / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 691759 / Symmetry type: POINT
RefinementHighest resolution: 3 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00465542
ELECTRON MICROSCOPYf_angle_d0.66888532
ELECTRON MICROSCOPYf_dihedral_angle_d4.7768636
ELECTRON MICROSCOPYf_chiral_restr0.04310146
ELECTRON MICROSCOPYf_plane_restr0.00411230

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