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: 2.8 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (ALPHA CHAIN)
A, D
180Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (BETA CHAIN)
B, E
188Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P04229 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P04229
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ENTEROTOXIN TYPE B PRECURSOR
C, F
13Influenza A virus (strain A/England/878/1969 H3N2)Mutation(s): 0 
Gene Names: HA
Find proteins for P04664 (Influenza A virus (strain A/England/878/1969 H3N2))
Go to UniProtKB:  P04664
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
B, E
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.205 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.600α = 90.00
b = 94.600β = 90.00
c = 247.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance