1PYW

Human class II MHC protein HLA-DR1 bound to a designed peptide related to influenza virus hemagglutinin, FVKQNA(MAA)AL, in complex with staphylococcal enterotoxin C3 variant 3B2 (SEC3-3B2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Exploration of the P6/P7 region of the peptide-binding site of the human class II Major Histocompatability Complex Protein HLA-DR1

Zavala-Ruiz, Z.Sundberg, E.J.Stone, J.D.DeOliveira, D.B.Chan, I.C.Svendsen, J.Mariuzza, R.A.Stern, L.J.

(2003) J Biol Chem 278: 44904-44912

  • DOI: https://doi.org/10.1074/jbc.M307652200
  • Primary Citation of Related Structures:  
    1PYW

  • PubMed Abstract: 

    Crystal structures of the class II major histocompatibilty complex (MHC) protein, HLA-DR1, generally show a tight fit between MHC and bound peptide except in the P6/P7 region of the peptide-binding site. In this region, there is a shallow water-filled pocket underneath the peptide and between the pockets that accommodate the P6 and P7 side chains. We investigated the properties of this pocket with the idea of engineering substitutions into the corresponding region of peptide antigens to increase their binding affinity for HLA-DR1. We investigated d-amino acids and N-alkyl modifications at both the P6 and P7 positions of the peptide and found that binding of peptides to HLA-DR1 could be increased by incorporating an N-methyl substitution at position 7 of the peptide. The crystal structure of HLA-DR1 bound to a peptide containing a P7 N-methyl alanine was determined. The N-methyl group orients in the P6/P7 pocket, displacing one of the waters usually bound in this pocket. The structure shows that the substitution does not alter the conformation of the bound peptide, which adopts the usual polyproline type II helix. An antigenic peptide carrying the N-methyl modification is taken up by antigen-presenting cells and loaded onto endogenous class II MHC molecules for presentation, and the resultant MHC-peptide complexes activate antigen-specific T-cells. These results suggest a possible strategy for increasing the affinity of weakly immunogenic peptides that might be applicable to the development of vaccines and diagnostic reagents.


  • Organizational Affiliation

    Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts 02139, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR-1 beta chain190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL10N/AMutation(s): 4 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
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Go to UniProtKB:  P03437
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UniProt GroupP03437
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Enterotoxin type C-3239Staphylococcus aureus subsp. aureus Mu50Mutation(s): 4 
Gene Names: ENTC3 OR SAV2009 OR SA1817
UniProt
Find proteins for P0A0L3 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P0A0L3 
Go to UniProtKB:  P0A0L3
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UniProt GroupP0A0L3
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MAA
Query on MAA
C
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.507α = 90
b = 172.507β = 90
c = 121.652γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2021-10-27
    Changes: Advisory, Database references, Derived calculations
  • Version 1.6: 2023-08-16
    Changes: Data collection, Refinement description