5AIU

A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for the Ring Catalyzed Synthesis of K63 Linked Ubiquitin Chains

Branigan, E.Plechanovova, A.Jaffray, E.Naismith, J.H.Hay, R.T.

(2015) Nat Struct Mol Biol 22: 597

  • DOI: 10.1038/nsmb.3052
  • Primary Citation of Related Structures:  
    5AIT, 5AIU

  • PubMed Abstract: 
  • RING E3 ligase-catalyzed formation of K63-linked ubiquitin chains by the Ube2V2-Ubc13 E2 complex is required in many important biological processes. Here we report the structure of the RING-domain dimer of rat RNF4 in complex with a human Ubc13∼Ub conjugate and Ube2V2 ...

    RING E3 ligase-catalyzed formation of K63-linked ubiquitin chains by the Ube2V2-Ubc13 E2 complex is required in many important biological processes. Here we report the structure of the RING-domain dimer of rat RNF4 in complex with a human Ubc13∼Ub conjugate and Ube2V2. The structure has captured Ube2V2 bound to the acceptor (priming) ubiquitin with K63 in a position favorable for attack on the linkage between Ubc13 and the donor (second) ubiquitin held in the active 'folded back' conformation by the RING domain of RNF4. We verified the interfaces identified in the structure by in vitro ubiquitination assays of site-directed mutants. To our knowledge, this represents the first view of synthesis of K63-linked ubiquitin chains in which both substrate ubiquitin and ubiquitin-loaded E2 are juxtaposed to allow E3 ligase-mediated catalysis.


    Organizational Affiliation

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE RNF4A133Rattus norvegicusMutation(s): 0 
Gene Names: Rnf4Snurf
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for O88846 (Rattus norvegicus)
Explore O88846 
Go to UniProtKB:  O88846
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 NB, D [auth E]154Homo sapiensMutation(s): 2 
Gene Names: UBE2NBLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
PHAROS:  P61088
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-CC, E [auth F]76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.19α = 90
b = 169.21β = 90
c = 52.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references, Structure summary
  • Version 1.2: 2015-08-19
    Changes: Database references
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 1.4: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations