5VNZ

Structure of a TRAF6-Ubc13~Ub complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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Literature

The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1.

Middleton, A.J.Budhidarmo, R.Das, A.Zhu, J.Foglizzo, M.Mace, P.D.Day, C.L.

(2017) Nat Commun 8: 1788-1788

  • DOI: 10.1038/s41467-017-01665-3
  • Primary Citation of Related Structures:  
    5VNZ, 5VO0

  • PubMed Abstract: 
  • Ubiquitin chains linked through lysine63 (K63) play a critical role in inflammatory signalling. Following ligand engagement of immune receptors, the RING E3 ligase TRAF6 builds K63-linked chains together with the heterodimeric E2 enzyme Ubc13-Uev1A. Dimerisation of the TRAF6 RING domain is essential for the assembly of K63-linked ubiquitin chains ...

    Ubiquitin chains linked through lysine63 (K63) play a critical role in inflammatory signalling. Following ligand engagement of immune receptors, the RING E3 ligase TRAF6 builds K63-linked chains together with the heterodimeric E2 enzyme Ubc13-Uev1A. Dimerisation of the TRAF6 RING domain is essential for the assembly of K63-linked ubiquitin chains. Here, we show that TRAF6 RING dimers form a catalytic complex where one RING interacts with a Ubc13~Ubiquitin conjugate, while the zinc finger 1 (ZF1) domain and linker-helix of the opposing monomer contact ubiquitin. The RING dimer interface is conserved across TRAFs and we also show that TRAF5-TRAF6 heterodimers form. Importantly, TRAF5 can provide ZF1, enabling ubiquitin transfer from a TRAF6-bound Ubc13 conjugate. Our study explains the dependence of activity on TRAF RING dimers, and suggests that both homo- and heterodimers mediated by TRAF RING domains have the capacity to synthesise ubiquitin chains.


    Organizational Affiliation

    Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand. catherine.day@otago.ac.nz.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TNF receptor-associated factor 6A, D118Danio rerioMutation(s): 0 
Gene Names: traf6si:dkey-56p7.3zgc:63704
EC: 2.3.2.27
UniProt
Find proteins for Q6IWL4 (Danio rerio)
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Go to UniProtKB:  Q6IWL4
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UniProt GroupQ6IWL4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NB, E157Homo sapiensMutation(s): 3 
Gene Names: UBE2NBLU
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
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Go to UniProtKB:  P61088
PHAROS:  P61088
GTEx:  ENSG00000177889 
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UniProt GroupP61088
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinC, F76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
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Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
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UniProt GroupP0CG47
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.36α = 90
b = 170.551β = 90
c = 97.312γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release