3MV9

Crystal Structure of the TK3-Gln55Ala TCR in complex with HLA-B*3501/HPVG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Allelic polymorphism in the T cell receptor and its impact on immune responses

Gras, S.Chen, Z.Miles, J.J.Liu, Y.C.Bell, M.J.Sullivan, L.C.Kjer-Nielsen, L.Brennan, R.M.Burrows, J.M.Neller, M.A.Khanna, R.Purcell, A.W.Brooks, A.G.McCluskey, J.Rossjohn, J.Burrows, S.R.

(2010) J.Exp.Med. 207: 1555-1567

  • DOI: 10.1084/jem.20100603
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for t ...

    In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for this phenomenon is undefined. We examined the T cell response to an HLA-B*3501-restricted epitope (HPVGEADYFEY) from Epstein-Barr virus (EBV), which is frequently dominated by a TRBV9*01(+) public TCR (TK3). However, the common allelic variant TRBV9*02, which differs by a single amino acid near the CDR2beta loop (Gln55-->His55), was never used in this response. The structure of the TK3 TCR, its allelic variant, and a nonnaturally occurring mutant (Gln55-->Ala55) in complex with HLA-B*3501(HPVGEADYFEY) revealed that the Gln55-->His55 polymorphism affected the charge complementarity at the TCR-peptide-MHC interface, resulting in reduced functional recognition of the cognate and naturally occurring variants of this EBV peptide. Thus, polymorphism in the TCR loci may contribute toward variability in immune responses and the outcome of infection.


    Organizational Affiliation

    The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-35 alpha chain
A
276Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P30685 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30685
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HPVG peptide from Epstein-Barr nuclear antigen 1
C
11Epstein-Barr virus (strain B95-8)Mutation(s): 0 
Gene Names: EBNA1
Find proteins for P03211 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P03211
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
alpha chain of the TK3 TCR
D
200N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
beta chain of the TK3 TCR
E
241N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.234 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.900α = 92.04
b = 62.570β = 102.29
c = 98.140γ = 109.18
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-20
    Type: Database references