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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE RNF4133Rattus norvegicusMutation(s): 0 
EC: 6.3.2
UniProt
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UniProt GroupO88846
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 N
B, E
154Homo sapiensMutation(s): 2 
EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
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PHAROS:  P61088
GTEx:  ENSG00000177889 
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UniProt GroupP61088
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
POLYUBIQUITIN-C
C, F
76Bos taurusMutation(s): 0 
UniProt
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
D, G
147Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15819 (Homo sapiens)
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PHAROS:  Q15819
GTEx:  ENSG00000169139 
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UniProt GroupQ15819
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  • Reference Sequence
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  (Full details and data files)

  • 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