3HCU

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TNF receptor-associated factor 6
A, C
118Homo sapiensMutation(s): 0 
Gene Names: TRAF6 (RNF85)
EC: 2.3.2.27
Find proteins for Q9Y4K3 (Homo sapiens)
Go to Gene View: TRAF6
Go to UniProtKB:  Q9Y4K3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
B, D
155Homo sapiensMutation(s): 0 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.493α = 90.00
b = 41.387β = 116.20
c = 123.745γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
ADSCdata collection
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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