LMP1 Protein binds to TRAF3 as a structural CD40

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

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LMP1 protein from the Epstein Barr virus is a structural CD40 decoy in B lymphocytes fro binding to TRAF3

Wu, S.D.Xie, P.Welsh, K.Li, C.Ni, C.-Z.Zhu, X.Reed, J.C.Satterthwait, A.C.Bishop, G.A.Ely, K.R.

(2005) J Biol Chem 39: 33620-33626

  • DOI: https://doi.org/10.1074/jbc.M502511200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Epstein-Barr virus is a human herpesvirus that causes infectious mononucleosis and lymphoproliferative malignancies. LMP1 (latent membrane protein-1), which is encoded by this virus and which is essential for transformation of B lymphocytes, acts as a constitutively active mimic of the tumor necrosis factor receptor (TNFR) CD40. LMP1 is an integral membrane protein containing six transmembrane segments and a cytoplasmic domain at the C terminus that binds to intracellular TNFR-associated factors (TRAFs). TRAFs are intracellular co-inducers of downstream signaling from CD40 and other TNFRs, and TRAF3 is required for activation of B lymphocytes by LMP1. Cytoplasmic C-terminal activation region 1 of LMP1 bears a motif (PQQAT) that conforms to the TRAF recognition motif PVQET in CD40. In this study, we report the crystal structure of this portion of LMP1 C-terminal activation region-1 (204PQQATDD210) bound in complex with TRAF3. The PQQAT motif is bound in the same binding crevice on TRAF3 where CD40 is bound, providing a molecular mechanism for LMP1 to act as a CD40 decoy for TRAF3. The LMP1 motif is presented in the TRAF3 crevice as a close structural mimic of the PVQET motif in CD40, and the intermolecular contacts are similar. However, the viral protein makes a unique contact: a hydrogen bond network formed between Asp210 in LMP1 and Tyr395 and Arg393 in TRAF3. This intermolecular contact is not made in the CD40-TRAF3 complex. The additional hydrogen bonds may stabilize the complex and strengthen the binding to permit LMP1 to compete with CD40 for binding to the TRAF3 crevice, influencing downstream signaling to B lymphocytes and contributing to dysregulated signaling by LMP1.

  • Organizational Affiliation

    Cancer Center, The Burnham Institute, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TNF receptor associated factor 3192Homo sapiensMutation(s): 0 
Gene Names: TRAF3CAP1CRAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13114 (Homo sapiens)
Explore Q13114 
Go to UniProtKB:  Q13114
PHAROS:  Q13114
GTEx:  ENSG00000131323 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13114
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Latent membrane protein 18N/AMutation(s): 0 
Find proteins for P13198 (Epstein-Barr virus (strain Raji))
Explore P13198 
Go to UniProtKB:  P13198
Entity Groups  
UniProt GroupP13198
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.67α = 90
b = 83.67β = 90
c = 77.96γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references