1QO3

Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Lectin-Like Natural Killer Cell Receptor Bound to its Mhc Class I Ligand

Tormo, J.Natarajan, K.Margulies, D.H.Mariuzza, R.A.

(1999) Nature 402: 623

  • DOI: 10.1038/45170

  • PubMed Abstract: 
  • Natural killer (NK) cell function is regulated by NK receptors that interact with MHC class I (MHC-I) molecules on target cells. The murine NK receptor Ly49A inhibits NK cell activity by interacting with H-2D(d) through its C-type-lectin-like NK rece ...

    Natural killer (NK) cell function is regulated by NK receptors that interact with MHC class I (MHC-I) molecules on target cells. The murine NK receptor Ly49A inhibits NK cell activity by interacting with H-2D(d) through its C-type-lectin-like NK receptor domain. Here we report the crystal structure of the complex between the Ly49A NK receptor domain and unglycosylated H-2D(d). The Ly49A dimer interacts extensively with two H-2D(d) molecules at distinct sites. At one interface, a single Ly49A subunit contacts one side of the MHC-I peptide-binding platform, presenting an open cavity towards the conserved glycosylation site on the H-2D(d) alpha2 domain. At a second, larger interface, the Ly49A dimer binds in a region overlapping the CD8-binding site. The smaller interface probably represents the interaction between Ly49A on the NK cell and MHC-I on the target cell, whereas the larger one suggests an interaction between Ly49A and MHC-I on the NK cell itself. Both Ly49A binding sites on MHC-I are spatially distinct from that of the T-cell receptor.


    Related Citations: 
    • 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.
      (1999) J.Mol.Biol. 283: 179
    • Interaction of the Nk Cell Inhibitory Receptor Ly49A with H-2Dd: Identification of a Site Distinct from the Tcr Site.
      Natarajan, K.,Boyd, L.F.,Schuck, P.,Yokoyama, W.M.,Eliat, D.,Margulies, D.H.
      (1999) Immunity 11: 591


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS I H-2DD HEAVY CHAIN
A
277Mus musculusGene Names: H2-D1
Find proteins for P01900 (Mus musculus)
Go to UniProtKB:  P01900
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2-MICROGLOBULIN
B
100Mus musculusGene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LY49A
C, D
137Mus musculusGene Names: Klra1 (Ly-49, Ly-49a, Ly49, Ly49A)
Find proteins for P20937 (Mus musculus)
Go to UniProtKB:  P20937
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.963α = 90.00
b = 96.957β = 90.00
c = 99.318γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-02
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2015-04-15
    Type: Database references