3HCU

Crystal structure of TRAF6 in complex with Ubc13 in the C2 space group

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 

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This is version 1.2 of the entry. See complete history. 


Literature

E2 interaction and dimerization in the crystal structure of TRAF6.

Yin, Q., Lin, S.C., Lamothe, B., Lu, M., Lo, Y.C., Hura, G., Zheng, L., Rich, R.L., Campos, A.D., Myszka, D.G., Lenardo, M.J., Darnay, B.G., Wu, H.

(2009) Nat Struct Mol Biol 16: 658-666

  • DOI: 10.1038/nsmb.1605
  • Primary Citation of Related Structures:  
    3HCS, 3HCT, 3HCU

  • PubMed Abstract: 

    • Tumor necrosis factor (TNF) receptor-associated factor (TRAF)-6 mediates Lys63-linked polyubiquitination for NF-kappaB activation via its N-terminal RING and zinc finger domains. Here we report the crystal structures of TRAF6 and its complex with the ubiquitin-conjugating enzyme (E2) Ubc13 ...

    Tumor necrosis factor (TNF) receptor-associated factor (TRAF)-6 mediates Lys63-linked polyubiquitination for NF-kappaB activation via its N-terminal RING and zinc finger domains. Here we report the crystal structures of TRAF6 and its complex with the ubiquitin-conjugating enzyme (E2) Ubc13. The RING and zinc fingers of TRAF6 assume a rigid, elongated structure. Interaction of TRAF6 with Ubc13 involves direct contacts of the RING and the preceding residues, and the first zinc finger has a structural role. Unexpectedly, this region of TRAF6 is dimeric both in the crystal and in solution, different from the trimeric C-terminal TRAF domain. Structure-based mutagenesis reveals that TRAF6 dimerization is crucial for polyubiquitin synthesis and autoubiquitination. Fluorescence resonance energy transfer analysis shows that TRAF6 dimerization induces higher-order oligomerization of full-length TRAF6. The mismatch of dimeric and trimeric symmetry may provide a mode of infinite oligomerization that facilitates ligand-dependent signal transduction of many immune receptors.

    Organizational Affiliation: 

    Weill Medical College of Cornell University, New York, New York, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TNF receptor-associated factor 6A, C118Homo sapiensMutation(s): 0 
Gene Names: RNF85, TRAF6
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4K3 (Homo sapiens)
Explore Q9Y4K3 
Go to UniProtKB:  Q9Y4K3
PHAROS:  Q9Y4K3
GTEx:  ENSG00000175104 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4K3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NB, D155Homo sapiensMutation(s): 0 
Gene Names: BLU, UBE2N
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
PHAROS:  P61088
GTEx:  ENSG00000177889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61088
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.493α = 90
b = 41.387β = 116.2
c = 123.745γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description