5AIT

A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 co ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE RNF4
A
133Rattus norvegicusMutation(s): 0 
Gene Names: Rnf4 (Snurf)
EC: 2.3.2.27
Find proteins for O88846 (Rattus norvegicus)
Go to UniProtKB:  O88846
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-CONJUGATING ENZYME E2 N
B, E
154Homo sapiensMutation(s): 2 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
POLYUBIQUITIN-C
C, F
76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Go to Gene View: UBC
Go to UniProtKB:  P0CH28
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
D, G
147Homo sapiensMutation(s): 0 
Gene Names: UBE2V2 (MMS2, UEV2)
Find proteins for Q15819 (Homo sapiens)
Go to Gene View: UBE2V2
Go to UniProtKB:  Q15819
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.580α = 90.00
b = 77.580β = 90.00
c = 328.840γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Database references, Other, Structure summary
  • Version 1.2: 2015-08-19
    Type: Database references