PDBsum entry: 1ddh

Complex (histocompatibility/antigen)

PDB id: 1ddh

Contents

Protein chains

274 a.a. *

99 a.a. *

Ligands

ARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE

Waters ×4

* Residue conservation analysis

PDB id:

1ddh

Name:

Complex (histocompatibility/antigen)

Title:

Mhc class i h-2dd heavy chain complexed with beta-2 microglobulin and an immunodominant peptide p18-i10 from the human immunodeficiency virus envelope glycoprotein 120

Structure:

Mhc class i h-2dd heavy chain. Chain: a. Fragment: extracellular domains. Engineered: yes. Mutation: yes. Beta-2 microglobulin. Chain: b. Fragment: extracellular domain. Engineered: yes.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: bl21. Cellular_location: extracellular. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Human immunodeficiency virus 1. Organism_taxid: 11676

Biol. unit:

Trimer (from PQS)

Resolution:

3.10Å R-factor: 0.229 R-free: 0.337

Authors:

H.Li,D.H.Margulies,R.A.Mariuzza

Key ref:

H.Li et al. (1998). Three-dimensional structure of H-2Dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120. J Mol Biol, 283, 179-191. PubMed id: 9761682 DOI: 10.1006/jmbi.1998.2091

Date:

22-Jun-98 Release date: 13-Jan-99

Protein chain

P01900  (HA12_MOUSE) -  H-2 class I histocompatibility antigen, D-D alpha chain

Seq: 365 a.a.

Struc: 274 a.a.*

Protein chain

P01887  (B2MG_MOUSE) -  Beta-2-microglobulin

Seq: 119 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (5 terms)
• Biological process: immune response (9 terms)
• Biochemical function: protein binding (1 term)

DOI no: 10.1006/jmbi.1998.2091

J Mol Biol 283:179-191 (1998)

PubMed id: 9761682

Three-dimensional structure of H-2Dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120.

H.Li, K.Natarajan, E.L.Malchiodi, D.H.Margulies, R.A.Mariuzza.

ABSTRACT

The crystal structure of the mouse major histocompatibility complex (MHC) class I molecule H-2Dd with an immunodominant peptide, designated P18-I10 (RGPGRAFVTI), from human immunodeficiency virus envelope glycoprotein 120 was determined at 3.2 A resolution. A novel orientation of the alpha3 domain of Dd relative to the alpha1/alpha2 domains results in significantly fewer contacts between alpha3 and beta2-microglobulin compared with other MHC class I proteins. Four out of ten peptide residues (P2 Gly, P3 Pro, P5 Arg and P10 Ile) are nearly completely buried in the Dd binding groove. This is consistent with previous findings that Dd exploits a four-residue binding motif comprising a glycine at P2, a proline at P3, a positively charged residue at P5, and a C-terminal hydrophobic residue at P9 or P10. The side-chain of P5 Arg is directed toward the floor of the predominantly hydrophobic binding groove where it forms two salt bridges and one hydrogen bond with Dd residue Asp77. The selection of glycine at P2 appears to be due to a narrowing of the B pocket, relative to that of other class I molecules, caused by Arg66 whose side-chain folds down into the binding cleft. Residue P3 Pro of P18-I10 occupies part of pocket D, which in Dd is partially split by a prominent hydrophobic ridge in the floor of the binding groove formed by Trp97 and Trp114. Residues P6 through P9 form a solvent-exposed bulge, with P7 Phe protruding the most from the binding groove and thereby probably constituting a major site of interaction with T cell receptors. A comparison of H-2Dd/P18-I10 with other MHC class I/peptide complexes of known structure provides insights into the possible basis for the specificity of the natural killer cell receptor Ly-49A for several related class I molecules.

Selected figure(s)

Figure 1.
Figure 1. Ribbon diagram of the H-2D^d/P18-I10 complex. The a1, a2, a3 and b[2]m domains are labeled. All Figures were generated by MOLSCRIPT [Kraulis 1991] and Raster3D [Bacon and Anderson 1988 and Merritt and Bacon 1997] if not specified.

Figure 6.
Figure 6. Location of H-2D^dresidues implicated in binding the NK inhibitory receptor Ly-49A. The P18-I10 peptide is yellow; the a1 and a2 domains of D^dare labeled. In pink are residues of in the a1 domain and N-terminal portion of the a2 domain of D^dthat differ in D^b. In blue are D^dresidues that have different side-chain conformations in Kb, Ldor D^b. In red is the N-terminal part of the a2 domain of D^d(residues 90 to 107).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 283, 179-191) copyright 1998.

Figures were selected by the author.