1A9B

DECAMER-LIKE CONFORMATION OF A NANO-PEPTIDE BOUND TO HLA-B3501 DUE TO NONSTANDARD POSITIONING OF THE C-TERMINUS

Summary for 1A9B

• Entry DOI: 10.2210/pdb1a9b/pdb
• Descriptor: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B*3501 (ALPHA CHAIN), BETA-2-MICROGLOBULIN, PEPTIDE LPPLDITPY (3 entities in total)
• Functional Keywords: mhc class i, histocompatibility complex, hla b3501, complex (mhc class i-peptide), complex (mhc class i-peptide) complex, complex (mhc class i/peptide)
• Biological source: Homo sapiens (human); More
• Cellular location: Membrane; Single-pass type I membrane protein: P30685; Secreted . Note=(Microbial infection) In the presence of M: P61769
• Total number of polymer chains: 6
• Total formula weight: 89869.76

Authors

Menssen, R.,Orth, P.,Ziegler, A.,Saenger, W. (deposition date: 1998-04-03, release date: 1998-10-21, Last modification date: 2024-10-09)

Primary citation

Menssen, R.,Orth, P.,Ziegler, A.,Saenger, W.
Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus.
J.Mol.Biol., 285:645-653, 1999

PubMed Abstract: The N and C termini of peptides presented by major histocompatibility complex (MHC) class I molecules are held within the peptide binding groove by a network of hydrogen bonds to conserved MHC residues. However, the published structure of the human allele HLA-B*3501 complexed with the nef octa-peptide VPLRPMTY, revealed non-standard positioning for both peptide termini. To investigate whether these deviations are indeed related to the length of the nef-peptide, we have determined the structure of HLA-B*3501 presenting a nona-peptide to 2.5 A resolution. A comparison of HLA-B*3501/peptide complexes with structures of other HLA molecules exhibits allele-specific properties of HLA-B*3501, as well as peptide-induced structural changes. Independent of the length of the bound peptide, HLA-B*3501 positions the peptide C terminus significantly closer to the alpha1-helix and nearer to the A pocket than observed for other HLA class I/peptide complexes. This reorientation is accompanied by a shift within the N-terminal part of the alpha2-helix towards the middle of the binding groove. Due to the short distance between the N and C termini, the nona-peptide is compressed and forced to zig-zag vertically within the binding groove. Its conformation rather resembles that of a deca-peptide than of other nona-peptides bound to class I molecules. Superposition of both HLA-B*3501/peptide complexes additionally reveals a significant, peptide-dependent deviation between the N-terminal parts of the alpha1-helices which might be due to different positioning of the peptide N termini. Taken together, these data illustrate the strong interdependence between the HLA class I molecule and the bound peptide.

PubMed: 9878435
DOI: 10.1006/jmbi.1998.2363

Experimental method

X-RAY DIFFRACTION (3.2 Å)