5YC1

TRAF4_GPIb complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.506 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for unique specificity of human TRAF4 for platelets GPIb beta and GPVI

Kim, C.M.Son, Y.J.Kim, S.Kim, S.Y.Park, H.H.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 11422-11427

  • DOI: 10.1073/pnas.1708688114

  • PubMed Abstract: 
  • Tumor necrosis factor (TNF)-receptor associated factor 4 (TRAF4), an adaptor protein with E3-ligase activity, is involved in embryogenesis, cancer initiation and progression, and platelet receptor (GPIb-IX-V complex and GPVI)-mediated signaling for r ...

    Tumor necrosis factor (TNF)-receptor associated factor 4 (TRAF4), an adaptor protein with E3-ligase activity, is involved in embryogenesis, cancer initiation and progression, and platelet receptor (GPIb-IX-V complex and GPVI)-mediated signaling for reactive oxygen species (ROS) production that initiates thrombosis at arterial shears. Disruption of platelet receptors and the TRAF4 interaction is a potential target for therapeutic intervention by antithrombotic drugs. Here, we report a crystal structure of TRAF4 (amino acid residues 290∼470) in complex with a peptide from the GPIbβ receptor (amino acid residues 177∼181). The GPIbβ peptide binds to a unique shallow surface composed of two hydrophobic pockets on TRAF4. Further studies revealed the TRAF4-binding motif Arg-Leu-X-Ala. The TRAF4-binding motif was present not only in platelet receptors but also in the TGF-β receptor. The current structure will provide a template for furthering our understanding of the receptor-binding specificity of TRAF4, TRAF4-mediated signaling, and related diseases.


    Organizational Affiliation

    School of Natural Science, Department of Chemistry and Biochemistry, Yeungnam University, Gyeongsan 712-749, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TNF receptor-associated factor 4
A, B, C, D, E, F
181Homo sapiensMutation(s): 0 
Gene Names: TRAF4 (CART1, MLN62, RNF83)
Find proteins for Q9BUZ4 (Homo sapiens)
Go to Gene View: TRAF4
Go to UniProtKB:  Q9BUZ4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GPIb peptide
G, I, K
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.506 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.716α = 90.00
b = 88.594β = 93.62
c = 120.757γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-06 
  • Released Date: 2017-10-11 
  • Deposition Author(s): Park, H.H., Kim, C.M.

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references