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- EMDB-52516: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term fo... -

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Basic information

Entry
Database: EMDB / ID: EMD-52516
TitleCryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term focused refinement)
Map data
Sample
  • Complex: UBR4/KCMF1 ubiquitin ligase complex
KeywordsUbiquitin ligase Protein quality control / LIGASE
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: 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
DepositionJan 10, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52516.png

Downloads & links

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Map

FileDownload / File: emd_52516.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.
= 487.68 Å		1.27 Å/pix.
x 384 pix.
= 487.68 Å		1.27 Å/pix.
x 384 pix.
= 487.68 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00234
Minimum - Maximum-0.0037277762 - 0.014396638
Average (Standard dev.)-0.00007816122 (±0.00042984015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 487.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52516_msk_1.map
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Half map: #1

Fileemd_52516_half_map_1.map
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Half map: #2

Fileemd_52516_half_map_2.map
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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

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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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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 / Details: Symmetry expanded particle set / Number images used: 225622
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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