6QZA

HLA-DR1 with GMF Influenza PB1 Peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

CD4+T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features.

Greenshields-Watson, A., Attaf, M., MacLachlan, B.J., Whalley, T., Rius, C., Wall, A., Lloyd, A., Hughes, H., Strange, K.E., Mason, G.H., Schauenburg, A.J., Hulin-Curtis, S.L., Geary, J., Chen, Y., Lauder, S.N., Smart, K., Vijaykrishna, D., Grau, M.L., Shugay, M., Andrews, R., Dolton, G., Rizkallah, P.J., Gallimore, A.M., Sewell, A.K., Godkin, A.J., Cole, D.K.

(2020) Cell Rep 32: 107885-107885

  • DOI: 10.1016/j.celrep.2020.107885
  • Primary Citation of Related Structures:  
    6QZA, 6QZC, 6QZD, 6R0E

  • PubMed Abstract: 

    • T cell recognition of peptides presented by human leukocyte antigens (HLAs) is mediated by the highly variable T cell receptor (TCR). Despite this built-in TCR variability, individuals can mount immune responses against viral epitopes by using identical or highly related TCRs expressed on CD8 + T cells ...

    T cell recognition of peptides presented by human leukocyte antigens (HLAs) is mediated by the highly variable T cell receptor (TCR). Despite this built-in TCR variability, individuals can mount immune responses against viral epitopes by using identical or highly related TCRs expressed on CD8 + T cells. Characterization of these TCRs has extended our understanding of the molecular mechanisms that govern the recognition of peptide-HLA. However, few examples exist for CD4 + T cells. Here, we investigate CD4 + T cell responses to the internal proteins of the influenza A virus that correlate with protective immunity. We identify five internal epitopes that are commonly recognized by CD4 + T cells in five HLA-DR1 + subjects and show conservation across viral strains and zoonotic reservoirs. TCR repertoire analysis demonstrates several shared gene usage biases underpinned by complementary biochemical features evident in a structural comparison. These epitopes are attractive targets for vaccination and other T cell therapies.

    Organizational Affiliation: 

    Cardiff University, School of Medicine, Heath Park, Cardiff, UK. Electronic address: coledk@cardiff.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA [auth AAA],
D [auth DDD]		183Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01903
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chainB [auth BBB],
E [auth EEE]		191Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PB1-410-422-GMF-PeptideC [auth CCC],
F [auth FFF]		20Influenza A virusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.017α = 90
b = 184.017β = 90
c = 87.285γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references