5VO0

Structure of a TRAF6-Ubc13~Ub complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
TNF receptor-associated factor 6
A, D
172Danio 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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 N
B, E
157Homo sapiensMutation(s): 3 
Gene Names: UBE2NBLU
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  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
Ubiquitin
C, F
76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
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UniProt GroupP0CG47
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.114α = 90
b = 181.114β = 90
c = 97.414γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MarsdenNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description