5VO0

Structure of a TRAF6-Ubc13~Ub complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41467-017-01665-3
  • Primary Citation of Related Structures:  

  • 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. ...

    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.,Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TNF receptor-associated factor 6
A, D
172Danio rerioMutation(s): 0 
Gene Names: traf6
EC: 2.3.2.27
Find proteins for Q6IWL4 (Danio rerio)
Go to UniProtKB:  Q6IWL4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
B, E
157Homo sapiensMutation(s): 3 
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
Ubiquitin
C, F
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.252 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 181.114α = 90.00
b = 181.114β = 90.00
c = 97.414γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MarsdenNew Zealand--

Revision History 

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