Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94.55 kDa 
• Atom Count: 6745 
• 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
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.70 Å
• R-Value Free: 0.331 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 

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:  
  3MV7, 3MV8, 3MV9


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P01889  Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS  P01889 GTEx  ENSG00000234745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HPVG peptide from Epstein-Barr nuclear antigen 1	C	11	N/A	Mutation(s): 0
Find proteins for P03211 (Epstein-Barr virus (strain B95-8)) Explore P03211  Go to UniProtKB:  P03211

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha chain of the TK3 TCR	D	200	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
beta chain of the TK3 TCR	E	241	Homo sapiens	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.331 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.9	α = 92.04
b = 62.57	β = 102.29
c = 98.14	γ = 109.18

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Database references