1FYT

CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELL RECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS II MOLECULE, HLA-DR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1.

Hennecke, J.Carfi, A.Wiley, D.C.

(2000) EMBO J 19: 5611-5624

  • DOI: https://doi.org/10.1093/emboj/19.21.5611
  • Primary Citation of Related Structures:  
    1FYT

  • PubMed Abstract: 

    An alphabeta T-cell receptor (alphabetaTCR)/hemagglutinin (HA) peptide/human leukocyte antigen (HLA)-DR1 complex was stabilized by flexibly linking the HA peptide with the human HA1.7 alphabetaTCR, to increase the local concentration of the interacting proteins once the peptide has been loaded onto the major histocompatibility complex (MHC) molecule. The structure of the complex, determined by X-ray crystallography, has a binding mode similar to that of the human B7 alphabetaTCR on a pMHCI molecule. Twelve of the 15 MHC residues contacted are at the same positions observed earlier in class I MHC/peptide/TCR complexes. One contact, to an MHC loop outside the peptide-binding site, is conserved and specific to pMHCII complexes. TCR gene usage in the response to HA/HLA-DR appears to conserve charged interactions between three lysines of the peptide and acidic residues on the TCR.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA.


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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ HA1 PEPTIDE CHAIN13H3N2 subtypeMutation(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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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR BETA CHAIN245Homo sapiensMutation(s): 1 
UniProt
Find proteins for P01850 (Homo sapiens)
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UniProt GroupP01850
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.902α = 90
b = 73.439β = 108.23
c = 122.428γ = 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: 2000-11-08
    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 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2021-11-03
    Changes: Database references, Structure summary