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)

Summary for 1PYW

• Entry DOI: 10.2210/pdb1pyw/pdb
• Related: 1DLH 1KLU
• Descriptor: HLA class II histocompatibility antigen, DR alpha chain, HLA class II histocompatibility antigen, DR-1 beta chain, 9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL, ... (5 entities in total)
• Functional Keywords: mhc class ii, major histocompatibility protein complex, hla-dr1, influenza, hemagglutinin, superantigen, antigen, immune system-protein binding-toxin complex, immune system/protein binding/toxin
• Biological source: Homo sapiens (human); More
• Cellular location: Cell membrane; Single-pass type I membrane protein: P01903
• Total number of polymer chains: 4
• Total formula weight: 71959.82

Authors

Zavala-Ruiz, Z.,Sundberg, E.J.,Stone, J.D.,DeOliveira, D.B.,Chan, I.C.,Svendsen, J.,Mariuzza, R.A.,Stern, L.J. (deposition date: 2003-07-09, release date: 2003-12-09, Last modification date: 2023-08-16)

Primary citation

Zavala-Ruiz, Z.,Sundberg, E.J.,Stone, J.D.,DeOliveira, D.B.,Chan, I.C.,Svendsen, J.,Mariuzza, R.A.,Stern, L.J.
Exploration of the P6/P7 region of the peptide-binding site of the human class II Major Histocompatability Complex Protein HLA-DR1
J.Biol.Chem., 278:44904-44912, 2003

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.

PubMed: 12952957
DOI: 10.1074/jbc.M307652200

Experimental method

X-RAY DIFFRACTION (2.1 Å)