3PQY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 U S A 108: 9536-9541

  • DOI: 10.1073/pnas.1106851108
  • Primary Citation of Related Structures:  
    3PQY

  • 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 is unclear ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chainAFKP275Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBGLQ99Mus musculusMutation(s): 1 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
10-mer peptide from RNA-directed RNA polymeraseCHMR10synthetic constructMutation(s): 0 
EC: 3.1
Find proteins for P13175 (Influenza A virus (strain A/Swine/Iowa/15/1930 H1N1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chainDINS195Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav21-dv12
Find proteins for K7N5N2 (Homo sapiens)
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Go to UniProtKB:  K7N5N2
Find proteins for A0A075B6C4 (Mus musculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
T cell receptor beta, variable 29,Human nkt tcr beta chainEJOT240Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trbv29
Find proteins for A0A0G2LB96 (Mus musculus)
Explore A0A0G2LB96 
Go to UniProtKB:  A0A0G2LB96
Find proteins for K7N5M4 (Homo sapiens)
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.893α = 90
b = 199.063β = 90
c = 202.465γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-06-18
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.4: 2020-02-12
    Changes: Database references, Source and taxonomy, Structure summary