1DDH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(1998) J.Mol.Biol. 283: 179-191

  • DOI: 10.1006/jmbi.1998.2091
  • Also Cited By: 1QO3

  • PubMed 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 reso ...

    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.


    Related Citations: 
    • H-2Dd Exploits a Four Residue Peptide Binding Motif
      Corr, M.,Boyd, L.F.,Padlan, E.A.,Margulies, D.H.
      (1993) J.Exp.Med. 178: 1877


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS I H-2DD HEAVY CHAIN
A
274Mus musculusGene Names: H2-D1
Find proteins for P01900 (Mus musculus)
Go to UniProtKB:  P01900
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2 MICROGLOBULIN
B
99Mus musculusGene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120
P
10Human immunodeficiency virus type 1 group M subtype BGene Names: env
Find proteins for P04582 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04582
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.330α = 90.00
b = 91.350β = 90.00
c = 108.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance