7R70

Crystal Structure of the UbArk2C fusion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ubiquitin and a charged loop regulate the ubiquitin E3 ligase activity of Ark2C.

Paluda, A.Middleton, A.J.Rossig, C.Mace, P.D.Day, C.L.

(2022) Nat Commun 13: 1181-1181

  • DOI: https://doi.org/10.1038/s41467-022-28782-y
  • Primary Citation of Related Structures:  
    7R70, 7R71

  • PubMed Abstract: 

    A large family of E3 ligases that contain both substrate recruitment and RING domains confer specificity within the ubiquitylation cascade. Regulation of RING E3s depends on modulating their ability to stabilise the RING bound E2~ubiquitin conjugate in the activated (or closed) conformation. Here we report the structure of the Ark2C RING bound to both a regulatory ubiquitin molecule and an activated E2~ubiquitin conjugate. The structure shows that the RING domain and non-covalently bound ubiquitin molecule together make contacts that stabilise the activated conformation of the conjugate, revealing why ubiquitin is a key regulator of Ark2C activity. We also identify a charged loop N-terminal to the RING domain that enhances activity by interacting with both the regulatory ubiquitin and ubiquitin conjugated to the E2. In addition, the structure suggests how Lys48-linked ubiquitin chains might be assembled by Ark2C and UbcH5b. Together this study identifies features common to RING E3s, as well elements that are unique to Ark2C and related E3s, which enhance assembly of ubiquitin chains.


  • Organizational Affiliation

    Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin,E3 ubiquitin-protein ligase RNF165
A, B
183Homo sapiensMutation(s): 0 
Gene Names: UBCRNF165
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZSG1 (Homo sapiens)
Explore Q6ZSG1 
Go to UniProtKB:  Q6ZSG1
PHAROS:  Q6ZSG1
GTEx:  ENSG00000141622 
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ6ZSG1P0CG48
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.47α = 90
b = 154.47β = 90
c = 81.706γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal Society of New ZealandNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description