1J8H

Crystal Structure of a Complex of a Human alpha/beta-T cell Receptor, Influenza HA Antigen Peptide, and MHC Class II Molecule, HLA-DR4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 

Starting Model: experimental
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Literature

Structure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity.

Hennecke, J.Wiley, D.C.

(2002) J Exp Med 195: 571-581

  • DOI: https://doi.org/10.1084/jem.20011194
  • Primary Citation of Related Structures:  
    1J8H

  • PubMed Abstract: 

    The alpha/beta T cell receptor (TCR) HA1.7 specific for the hemagglutinin (HA) antigen peptide from influenza A virus is HLA-DR1 restricted but cross-reactive for the HA peptide presented by the allo-major histocompatibility complex (MHC) class II molecule HLA-DR4. We report here the structure of the HA1.7/DR4/HA complex, determined by X-ray crystallography at a resolution of 2.4 A. The overall structure of this complex is very similar to the previously reported structure of the HA1.7/DR1/HA complex. Amino acid sequence differences between DR1 and DR4, which are located deep in the peptide binding groove and out of reach for direct contact by the TCR, are able to indirectly influence the antigenicity of the pMHC surface by changing the conformation of HA peptide residues at position P5 and P6. Although TCR HA1.7 is cross-reactive for HA presented by DR1 and DR4 and tolerates these conformational differences, other HA-specific TCRs are sensitive to these changes. We also find a dependence of the width of the MHC class II peptide-binding groove on the sequence of the bound peptide by comparing the HA1.7/DR4/HA complex with the structure of DR4 presenting a collagen peptide. This structural study of TCR cross-reactivity emphasizes how MHC sequence differences can affect TCR binding indirectly by moving peptide atoms.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. jens.hennecke@Micromet.de


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN181Homo sapiensMutation(s): 0 
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PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P01903-1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-4 BETA CHAIN192Homo sapiensMutation(s): 0 
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Find proteins for P01911 (Homo sapiens)
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PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01911-1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ HA1 PEPTIDE CHAIN13AlphainfluenzavirusMutation(s): 0 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
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UniProt GroupP03437
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR ALPHA CHAIN212Homo sapiensMutation(s): 0 
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Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR BETA CHAIN246Homo sapiensMutation(s): 1 
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Find proteins for P01850 (Homo sapiens)
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UniProt GroupP01850
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.753α = 90
b = 73.317β = 108.52
c = 123.033γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-16
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-16
    Changes: Structure summary