Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.25 kDa 
• Atom Count: 4096 
• Modelled Residue Count: 495 
• Deposited Residue Count: 549 
• Unique protein chains: 1

4M4E

TRAF domain of human TRAF4

• PDB DOI: 10.2210/pdb4M4E/pdb

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


• Deposited: 2013-08-07 Released: 2013-09-11 
• Deposition Author(s): Niu, F., Ru, H., Ding, W., Ouyang, S., Liu, Z.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.200 
• R-Value Observed: 0.208 

Literature

Structural biology study of human TNF receptor associated factor 4 TRAF domain

Niu, F., Ru, H., Ding, W., Ouyang, S., Liu, Z.J.

(2013) Protein Cell 4: 687-694

• PubMed: 23982741 
• DOI: 10.1007/s13238-013-3068-z
• Primary Citation of Related Structures:  
  4M4E


• PubMed Abstract: 
  

TRAF4 is a unique member of TRAF family, which is essential for innate immune response, nervous system and other systems. In addition to be an adaptor protein, TRAF4 was identified as a regulator protein in recent studies. We have determined the crystal structure of TRAF domain of TRAF4 (residues 292-466) at 2.60 Å resolution by X-ray crystallography method. The trimericly assembled TRAF4 resembles a mushroom shape, containing a super helical "stalk" which is made of three right-handed intertwined α helixes and a C-terminal "cap", which is divided at residue L302 as a boundary. Similar to other TRAFs, both intermolecular hydrophobic interaction in super helical "stalk" and hydrogen bonds in "cap" regions contribute directly to the formation of TRAF4 trimer. However, differing from other TRAFs, there is an additional flexible loop (residues 421-426), which contains a previously identified phosphorylated site S426 exposing on the surface. This S426 was reported to be phosphorylated by IKKα which is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB activation. Therefore, the crystal structure of TRAF4-TRAF is valuable for understanding its molecular basis for its special function and provides structural information for further studies.

---

Organizational Affiliation: 

Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TNF receptor-associated factor 4	A, B, C	183	Homo sapiens	Mutation(s): 0  Gene Names: TRAF4, CART1, MLN62, RNF83
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUZ4 (Homo sapiens) Explore Q9BUZ4  Go to UniProtKB:  Q9BUZ4
PHAROS:  Q9BUZ4 GTEx:  ENSG00000076604

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.200 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.295	α = 90
b = 88.205	β = 90
c = 118.425	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-07 
• Released Date: 2013-09-11 
Deposition Author(s): Niu, F., Ru, H., Ding, W., Ouyang, S., Liu, Z.J.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release