1DLH

CRYSTAL STRUCTURE OF THE HUMAN CLASS II MHC PROTEIN HLA-DR1 COMPLEXED WITH AN INFLUENZA VIRUS PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide.

Stern, L.J.Brown, J.H.Jardetzky, T.S.Gorga, J.C.Urban, R.G.Strominger, J.L.Wiley, D.C.

(1994) Nature 368: 215-221

  • DOI: 10.1038/368215a0
  • Primary Citation of Related Structures:  
    1DLH

  • PubMed Abstract: 
  • An influenza virus peptide binds to HLA-DR1 in an extended conformation with a pronounced twist. Thirty-five per cent of the peptide surface is accessible to solvent and potentially available for interaction with the antigen receptor on T cells. Pock ...

    An influenza virus peptide binds to HLA-DR1 in an extended conformation with a pronounced twist. Thirty-five per cent of the peptide surface is accessible to solvent and potentially available for interaction with the antigen receptor on T cells. Pockets in the peptide-binding site accommodate five of the thirteen side chains of the bound peptide, and explain the peptide specificity of HLA-DR1. Twelve hydrogen bonds between conserved HLA-DR1 residues and the main chain of the peptide provide a universal mode of peptide binding, distinct from the strategy used by class I histocompatibility proteins.


    Related Citations: 
    • Three-Dimensional Structure of the Human Class II Histocompatibility Antigen Hla-Dr1
      Brown, J.H., Jardetzky, T.S., Gorga, J.C., Stern, L.J., Urban, R.G., Strominger, J.L., Wiley, D.C.
      (1993) Nature 364: 33

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Harvard University, Cambridge Massachusetts 62138.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (ALPHA CHAIN)AD180Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ENTEROTOXIN TYPE B PRECURSORCF13N/AMutation(s): 0 
Find proteins for P04664 (Influenza A virus (strain A/England/878/1969 H3N2))
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Go to UniProtKB:  P04664
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (BETA CHAIN)BE188Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
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PHAROS  P01911
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
2 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, D, E
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: 2.80 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.6α = 90
b = 94.6β = 90
c = 247.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1994-02-15 
  • Released Date: 1994-06-22 
  • Deposition Author(s): Stern, L.J.

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    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, Derived calculations, Other, Structure summary