Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 94.61 kDa 
• Atom Count: 6833 
• Residue Count: 824 
• Unique protein chains: 5

2VLK

The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain

• DOI: 10.2210/pdb2VLK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, unidentified influenza virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-15 Released: 2008-01-22 
• Deposition Author(s): Ishizuka, J., Stewart-Jones, G., Van Der Merwe, A., Bell, J., Mcmichael, A., Jones, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.288 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Literature

The Structural Dynamics and Energetics of an Immunodominant T-Cell Receptor are Programmed by its Vbeta Domain

Ishizuka, J., Stewart-Jones, G., Van Der Merwe, A., Bell, J., Mcmichael, A., Jones, Y.

(2008) Immunity 28: 171

• PubMed: 18275829 
• DOI: 10.1016/j.immuni.2007.12.018
• Primary Citation of Related Structures:  
  2VLL, 2VLM, 2VLR, 2VLJ, 2VLK


• PubMed Abstract: 
  

Immunodominant and public T cell receptor (TCR) usage is relatively common in many viral diseases yet surprising in the context of the large naive TCR repertoire. We examined the highly conserved Vbeta17:Valpha10.2 JM22 T cell response to the influenza matrix peptide (58-66)-HLA-A*0201 (HLA-A2-flu) through extensive kinetic, thermodynamic, and structural analyses. We found several conformational adjustments that accompany JM22-HLA-A2-flu binding and identified a binding "hotspot" within the Vbeta domain of the TCR. Within this hotspot, key germline-encoded CDR1 and CDR2 loop residues and a crucial but commonly coded residue in the hypervariable region of CDR3 provide the basis for the substantial bias in the selection of the germline-encoded Vbeta17 domain. The chances of having a substantial number of T cells in the naive repertoire that have HLA-A2-flu-specific Vbeta17 receptors may consequently be relatively high, thus explaining the immunodominant usage of this clonotype.

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Organizational Affiliation: 

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439 GTEx  ENSG00000206503

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
FLU MATRIX PEPTIDE	C	9	unidentified influenza virus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
JM22 TCR ALPHA CHAIN	D	201	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
JM22 TCR BETA CHAIN	E	244	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.288 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.8	α = 90
b = 47.892	β = 112.34
c = 112.819	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-15 
• Released Date: 2008-01-22 
Deposition Author(s): Ishizuka, J., Stewart-Jones, G., Van Der Merwe, A., Bell, J., Mcmichael, A., Jones, Y.

Revision History 

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance