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: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1074/jbc.M307652200

  • 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-fille ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
182Homo 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
HLA class II histocompatibility antigen, DR-1 beta chain
B
190Homo 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
9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL
C
10Influenza A virus (strain A/Aichi/2/1968 H3N2)Mutation(s): 4 
Gene Names: HA
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Go to UniProtKB:  P03437
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Enterotoxin type C-3
D
239Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 4 
Gene Names: entC3
Find proteins for P0A0L3 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P0A0L3
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MAA
Query on MAA
C
L-peptide linkingC4 H9 N O2ALA
ACE
Query on ACE
C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 172.507α = 90.00
b = 172.507β = 90.00
c = 121.652γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345data collection
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description
  • Version 1.4: 2018-04-04
    Type: Data collection