4K8U

Crystal structure of TRAF4 TRAF domain

• PDB DOI: https://doi.org/10.2210/pdb4K8U/pdb

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


• Deposited: 2013-04-18 Released: 2014-01-15 
• Deposition Author(s): Park, H.H., Yoon, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 

Literature

Structure of the TRAF4 TRAF domain with a coiled-coil domain and its implications for the TRAF4 signalling pathway.

Yoon, J.H., Cho, Y.J., Park, H.H.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2-10

• PubMed: 24419373 
• DOI: https://doi.org/10.1107/S139900471302333X
• Primary Citation of Related Structures:  
  4K8U


• PubMed Abstract: 
  

  The TNF receptor-associated factor (TRAF) proteins are structurally similar scaffold proteins that mediate between members of the TNF receptor (TNFR) family and downstream effector molecules such as kinases in the immune signalling pathway. Seven TRAFs have been identified, including TRAF4, which is a unique member that participates in many ontogenic processes, including nerve-system development. TRAFs commonly contain the TRAF domain, which mediates interaction with target receptors and effectors. As a first step towards elucidating the molecular mechanisms of the TRAF4-mediated signalling pathway, the first crystal structure of the human TRAF4 TRAF domain with a coiled-coil domain is reported at 2.3 Å resolution.

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Organizational Affiliation: 

School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.49 kDa 
• Atom Count: 4,340 
• Modelled Residue Count: 530 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TNF receptor-associated factor 4	A, B, C	198	Homo sapiens	Mutation(s): 0  Gene Names: TRAF4
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: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.949	α = 90
b = 87.989	β = 90
c = 117.364	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

• Released Date: 2014-01-15 
Deposition Author(s): Park, H.H., Yoon, J.H.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Data collection
• Version 1.2: 2020-01-01
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references