3PQY

Crystal Structure of 6218 TCR in complex with the H2Db-PA224

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.192 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structural basis for enabling T-cell receptor diversity within biased virus-specific CD8+ T-cell responses

Day, E.B., Guillonneau, C., Gras, S., La Gruta, N.L., Vignali, D.A.A., Doherty, P.C., Purcell, A.W., Rossjohn, J., Turner, S.J.

(2011) Proc.Natl.Acad.Sci.USA 108: 9536-9541

  • DOI: 10.1073/pnas.1106851108

  • PubMed Abstract: 

    • Pathogen-specific responses are characterized by preferred profiles of peptide+class I MHC (pMHCI) glycoprotein-specific T-cell receptor (TCR) Variable (V)-region use. How TCRV-region bias impacts TCRαβ heterodimer selection and resultant diversity i ...

    Pathogen-specific responses are characterized by preferred profiles of peptide+class I MHC (pMHCI) glycoprotein-specific T-cell receptor (TCR) Variable (V)-region use. How TCRV-region bias impacts TCRαβ heterodimer selection and resultant diversity is unclear. The D(b)PA(224)-specific TCR repertoire in influenza A virus-infected C57BL/6J (B6) mice exhibits a preferred TCRV-region bias toward the TRBV29 gene segment and an optimal complementarity determining region (CDR3) β-length of 6 aa. Despite these restrictions, D(b)PA(224)-specific BV29(+) T cells use a wide array of unique CDR3β sequences. Structural characterization of a single, TRBV29(+)D(b)P(A224)-specific TCRαβ-pMHCI complex demonstrated that CDR3α amino acid side chains made specific peptide interactions, but the CDR3β main chain exclusively contacted peptides. Thus, length but not amino acid sequence was key for recognition and flexibility in Vβ-region use. In support of this hypothesis, retrovirus expression of the D(b)PA(224)-specific TCRVα-chain was used to constrain pairing within a naive/immune epitope-specific repertoire. The retrogenic TCRVα paired with a diversity of CDR3βs in the context of a preferred TCRVβ spectrum. Overall, these data provide an explanation for the combination of TCRV region bias and diversity within selected repertoires, even as they maintain exquisite pMHCI specificity.

    Organizational Affiliation: 

    Department of Microbiology and Immunology, Bio21, Department of Biochemistry, University of Melbourne, Parkville, VIC 3010, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, D-B alpha chain
A, F, K, P
275Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Go to UniProtKB:  P01899
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, G, L, Q
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
10-mer peptide from RNA-directed RNA polymerase
C, H, M, R
10Influenza A virus (strain A/Swine/Iowa/15/1930 H1N1)Mutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for P13175 (Influenza A virus (strain A/Swine/Iowa/15/1930 H1N1))
Go to UniProtKB:  P13175
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
alpha chain of the 6218-TCR
D, I, N, S
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
beta chain of the 6218-TCR
E, J, O, T
240N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.192 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.893α = 90.00
b = 199.063β = 90.00
c = 202.465γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
DENZOdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-06-18
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Advisory, Refinement description