Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94552.57 
• Atom Count: 6683 
• Residue Count: 828 
• Unique protein chains: 5

3MV9

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

• DOI: 10.2210/pdb3MV9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Epstein-Barr virus (strain B95-8)
• Expression System: Escherichia coli


• Deposited: 2010-05-03 Released: 2010-06-09 
• Deposition Author(s): 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.

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Experimental Data Snapshot

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

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

• PubMed: 20566715 
• DOI: 10.1084/jem.20100603
• Primary Citation of Related Structures:  
  3MV8, 3MV7


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, B-35 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B (HLAB)
Find proteins for P01889 (Homo sapiens) Go to Gene View: HLA-B Go to UniProtKB:  P01889

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HPVG peptide from Epstein-Barr nuclear antigen 1	C	11	Epstein-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
Molecule	Chains	Sequence Length	Organism	Details
alpha chain of the TK3 TCR	D	200	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
beta chain of the TK3 TCR	E	241	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 44.900	α = 92.04
b = 62.570	β = 102.29
c = 98.140	γ = 109.18

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PHASER	phasing
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-03 
• Released Date: 2010-06-09 
• Deposition Author(s): 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.

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