Crystal structure of the E3 module from UBR4

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

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UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4.

Barnsby-Greer, L.Mabbitt, P.D.Dery, M.A.Squair, D.R.Wood, N.T.Lamoliatte, F.Lange, S.M.Virdee, S.

(2024) Nat Struct Mol Biol 31: 351-363

  • DOI: https://doi.org/10.1038/s41594-023-01192-4
  • Primary Citation of Related Structures:  
    8B5W, 8BTL

  • PubMed Abstract: 

    UBR4 is a 574 kDa E3 ligase (E3) of the N-degron pathway with roles in neurodevelopment, age-associated muscular atrophy and cancer. The catalytic module that carries out ubiquitin (Ub) transfer remains unknown. Here we identify and characterize a distinct E3 module within human UBR4 consisting of a 'hemiRING' zinc finger, a helical-rich UBR zinc-finger interacting (UZI) subdomain, and an N-terminal region that can serve as an affinity factor for the E2 conjugating enzyme (E2). The structure of an E2-E3 complex provides atomic-level insight into the specificity determinants of the hemiRING toward the cognate E2s UBE2A/UBE2B. Via an allosteric mechanism, the UZI subdomain modestly activates the Ub-loaded E2 (E2∼Ub). We propose attenuated activation is complemented by the intrinsically high lysine reactivity of UBE2A, and their cooperation imparts a reactivity profile important for substrate specificity and optimal degradation kinetics. These findings reveal the mechanistic underpinnings of a neuronal N-degron E3, its specific recruitment of UBE2A, and highlight the underappreciated architectural diversity of cross-brace domains with Ub E3 activity.

  • Organizational Affiliation

    MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA459Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T4S7 (Homo sapiens)
Explore Q5T4S7 
Go to UniProtKB:  Q5T4S7
GTEx:  ENSG00000127481 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5T4S7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.131α = 90
b = 84.644β = 90
c = 148.13γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
DIALSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references