ISDA

Deposition Date 2008-01-15

Release Date 2008-01-22

Last Version Date 2024-10-09

Entry Detail

PDB ID:

2VLK

Keywords:

IMMUNE SYSTEM

Title:

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

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)
UNIDENTIFIED INFLUENZA VIRUS (Taxon ID: 11309)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.50 Å

R-Value Free:

0.28

R-Value Work:

0.21

R-Value Observed:

0.22

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
Chain IDs:A
Chain Length:276
Number of Molecules:1
Biological Source:HOMO SAPIENS

UniProt ID:P04439 Pfam ID:PF00129, PF07654

Protein Blast

Polymer Type:polypeptide(L)
Molecule:BETA-2-MICROGLOBULIN
Gene (Uniprot):B2M
Chain IDs:B
Chain Length:100
Number of Molecules:1
Biological Source:HOMO SAPIENS

UniProt ID:P61769 Pfam ID:PF07654

Polymer Type:polypeptide(L)
Molecule:FLU MATRIX PEPTIDE
Chain IDs:C
Chain Length:9
Number of Molecules:1
Biological Source:UNIDENTIFIED INFLUENZA VIRUS

Polymer Type:polypeptide(L)
Molecule:JM22 TCR ALPHA CHAIN
Chain IDs:D
Chain Length:201
Number of Molecules:1
Biological Source:HOMO SAPIENS

Polymer Type:polypeptide(L)
Molecule:JM22 TCR BETA CHAIN
Chain IDs:E
Chain Length:244
Number of Molecules:1
Biological Source:HOMO SAPIENS

Primary Citation

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.Show

Immunity 28 171 ? (2008)

PMID: 18275829 DOI: 10.1016/J.IMMUNI.2007.12.018

Abstact

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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