Crystal structure of the major histocompatibility complex class I H-2Kb molecule containing a single viral peptide: implications for peptide binding and T-cell receptor recognition.

Abstract

To study the structure of a homogenous major histocompatibility complex (MHC) class I molecule containing a single bound peptide, a complex of recombinant mouse H-2Kb, beta 2-microglobulin (beta 2m), and a fragment of the vesicular stomatitis virus (VSV) nuclear capsid protein, VSV-(N52-59) octapeptide (Arg-Gly-Tyr-Val-Tyr-Gln-Gly-Leu), was prepared by exploiting a high-yield bacterial expression system and in vitro cocomplex formation. The structure of mouse H-2Kb revealed its similarity to three human class I HLA molecules, consistent with the high primary sequence homology and common function of these peptide-presenting molecules. Electron density was located in the peptide-binding groove, to which a single peptide in a unique conformation was unambiguously fit. The peptide extends the length of the groove, parallel to the alpha-helices, and assumes an extended, mostly beta-strand conformation. The peptide is constrained within the groove by hydrogen bonding of its main-chain atoms and by contacts of its side chains with the H-2Kb molecule. The amino-terminal nitrogen atom of the peptide forms a hydrogen bond with the hydroxyl group of Tyr-171 of H-2Kb at one end of the groove, while the carboxyl-terminal oxygen forms a hydrogen bond with the hydroxyl group of Tyr-84 at the other end. Since the amino acids at both ends are conserved among human and mouse MHC molecules, this anchoring of each end of the peptide appears to be a general feature of peptide-MHC class I molecule binding and imposes restrictions on its length. The side chains of residues Tyr-3, Tyr-5, and Leu-8 of the VSV octapeptide fit into the interior of the H-2Kb molecule with no appreciable surface exposure, a finding in support of previous biological studies that showed the importance of these residues for binding. Thus, the basis for binding of specific peptide sequences to the MHC class I molecule is the steric restriction imposed on the peptide side chains by the architecture of the floor and sides of the groove. The side chains of Arg-1, Val-4, and Gln-6 and the main-chain of Gly-7 of the octapeptide are exposed on the surface of the complex, thus confirming their availability for T-cell receptor contact, as previously demonstrated by T-cell recognition experiments.

Altered Peptide Ligand-Mediated TCR Antagonism Can Be Modulated by a Change in a Single Amino Acid Residue Within the CDR3β of an MHC Class I-Restricted TCR

“…Amino acid side chains at position 1 and 6 of VSV peptide are solvent exposed and make contact with H-2K b /VSV-specific TCRs (35)(36)(37). As shown in Fig.…”

TCR Binding Kinetics Measured with MHC Class I Tetramers Reveal a Positive Selecting Peptide with Relatively High Affinity for TCR

“…H-2D b H chain containing a biotinylation sequence (25) and human ␤ 2 -microglobulin L chain were individually produced in Escherichia coli and refolded as described previously (35). Inclusion bodies were dissolved in 8 M urea and mixed with peptide using 4.5 mg H chain:1.5 mg L:1 mg peptide in the presence of 10 mM DTT.…”

Production and crystallization of MHC class I B allele single peptide complexes

“…Much of our understanding ot peptide binding to class I molecules has come from a complementary combination of analysis of X-ray crystallographic sl ructures and identification of naturally bound peptides [3]. The first class I structure, HLA A2 [4], together with subseqtlent structural analysis of other human class I alleles [5][6][7][8][9][10][11] aad murine alleles [12][13][14][15] complexed with single peptides, revealed general principles for peptide binding to class I molemles. These structures show that peptides are held in the class I binding groove at the N-and C-termini by a conserved network of hydrogen bonds and by the binding of conserved rcsidues (anchor residues) in pockets lined by polymorphic /~HC residues (review [16]).…”