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 

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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: 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 mo ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAINA181Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
GTEx  ENSG00000204287
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-4 BETA CHAINB192Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
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Go to UniProtKB:  P01911
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PHAROS  P01911
GTEx  ENSG00000196126
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HEMAGGLUTININ HA1 PEPTIDE CHAINC13AlphainfluenzavirusMutation(s): 0 
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL RECEPTOR ALPHA CHAIND212Homo sapiensMutation(s): 0 
Gene Names: TRAC, TCRA
Find proteins for P01848 (Homo sapiens)
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PHAROS  P01848
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL RECEPTOR BETA CHAINE246Homo sapiensMutation(s): 1 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
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 

  • 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