Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.82 kDa 
• Atom Count: 4098 
• Residue Count: 509 
• Unique protein chains: 2

3HCU

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

• DOI: 10.2210/pdb3HCU/pdb

• Classification: SIGNALING PROTEIN/LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-06 Released: 2009-05-26 
• Deposition Author(s): 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.

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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 

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

• PubMed: 19465916 
• DOI: 10.1038/nsmb.1605
• Structures With Same Primary Citation


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TNF receptor-associated factor 6	A, C	118	Homo sapiens	Mutation(s): 0  Gene Names: RNF85, TRAF6 EC: 2.3.2.27
Find proteins for Q9Y4K3 (Homo sapiens) Explore Q9Y4K3  Go to UniProtKB:  Q9Y4K3
NIH Common Fund Data Resources
PHAROS  Q9Y4K3 GTEx  ENSG00000175104

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 N	B, D	155	Homo sapiens	Mutation(s): 0  Gene Names: BLU, UBE2N EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS  P61088 GTEx  ENSG00000177889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 130.493	α = 90
b = 41.387	β = 116.2
c = 123.745	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-06 
• Released Date: 2009-05-26 
Deposition Author(s): 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.

Revision History 

• 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