5AIT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 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
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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)
Find proteins for O88846 (Rattus norvegicus)
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Go to UniProtKB:  O88846
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 NBE154Homo sapiensMutation(s): 2 
Gene Names: UBE2NBLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P61088
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-CCF76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2DG147Homo sapiensMutation(s): 0 
Gene Names: UBE2V2MMS2UEV2
Find proteins for Q15819 (Homo sapiens)
Explore Q15819 
Go to UniProtKB:  Q15819
NIH Common Fund Data Resources
PHAROS  Q15819
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.58α = 90
b = 77.58β = 90
c = 328.84γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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