1T5X

HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2

Summary for 1T5X

• Entry DOI: 10.2210/pdb1t5x/pdb
• Related: 1AQD 1DLH 1KLU 1PYW 1T5W
• Descriptor: HLA class II histocompatibility antigen, DR alpha chain, HLA class II histocompatibility antigen, DRB1-1 beta chain, 15-mer peptide fragment of Regulatory protein MIG1, ... (5 entities in total)
• Functional Keywords: mhc class ii; major histocompatibiloty complex protein; hla-dr1; superantigen; antigen; peptide, immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Cell membrane; Single-pass type I membrane protein: P01903 P04229; Nucleus: P27705; Secreted: P0A0L5
• Total number of polymer chains: 4
• Total formula weight: 72448.27

Authors

Zavala-Ruiz, Z.,Strug, I.,Anderson, M.W.,Gorski, J.,Stern, L.J. (deposition date: 2004-05-05, release date: 2004-08-17, Last modification date: 2024-10-16)

Primary citation

Zavala-Ruiz, Z.,Strug, I.,Anderson, M.W.,Gorski, J.,Stern, L.J.
A Polymorphic Pocket at the P10 Position Contributes to Peptide Binding Specificity in Class II MHC Proteins
Chem.Biol., 11:1395-1402, 2004

PubMed Abstract: Peptides bind to class II major histocompatibility complex (MHC) proteins in an extended conformation. Pockets in the peptide binding site spaced to accommodate peptide side chains at the P1, P4, P6, and P9 positions have been previously characterized and help to explain the obtained peptide binding specificity. However, two peptides differing only at P10 have significantly different binding affinities for HLA-DR1. The structure of HLA-DR1 in complex with the tighter binding peptide shows that the peptide binds in the usual polyproline type II conformation, but with the P10 residue accommodated in a shallow pocket at the end of the binding groove. HLA-DR1 variants with polymorphic residues at these positions were produced and found to exhibit different side chain specificity at the P10 position. These results define a new specificity position in HLA-DR proteins.

PubMed: 15489166
DOI: 10.1016/j.chembiol.2004.08.007

Experimental method

X-RAY DIFFRACTION (2.5 Å)