1EFX

STRUCTURE OF A COMPLEX BETWEEN THE HUMAN NATURAL KILLER CELL RECEPTOR KIR2DL2 AND A CLASS I MHC LIGAND HLA-CW3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand.

Boyington, J.C.Motyka, S.A.Schuck, P.Brooks, A.G.Sun, P.D.

(2000) Nature 405: 537-543

  • DOI: 10.1038/35014520

  • PubMed Abstract: 
  • Target cell lysis is regulated by natural killer (NK) cell receptors that recognize class I MHC molecules. Here we report the crystal structure of the human immunoglobulin-like NK cell receptor KIR2DL2 in complex with its class I ligand HLA-Cw3 and p ...

    Target cell lysis is regulated by natural killer (NK) cell receptors that recognize class I MHC molecules. Here we report the crystal structure of the human immunoglobulin-like NK cell receptor KIR2DL2 in complex with its class I ligand HLA-Cw3 and peptide. KIR binds in a nearly orthogonal orientation across the alpha1 and alpha2 helices of Cw3 and directly contacts positions 7 and 8 of the peptide. No significant conformational changes in KIR occur on complex formation. The receptor footprint on HLA overlaps with but is distinct from that of the T-cell receptor. Charge complementarity dominates the KIR/HLA interface and mutations that disrupt interface salt bridges substantially diminish binding. Most contacts in the complex are between KIR and conserved HLA-C residues, but a hydrogen bond between Lys 44 of KIR2DL2 and Asn 80 of Cw3 confers the allotype specificity. KIR contact requires position 8 of the peptide to be a residue smaller than valine. A second KIR/HLA interface produced an ordered receptor-ligand aggregation in the crystal which may resemble receptor clustering during immune synapse formation.


    Related Citations: 
    • Crystal Structure of the HLA-Cw3 Allotype-specific Killer Cell Inhibitory Receptor KIR2DL2
      Snyder, G.A.,Brooks, A.G.,Sun, P.D.
      (1999) Proc.Natl.Acad.Sci.USA 96: 3864


    Organizational Affiliation

    Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA-CW3 (HEAVY CHAIN)
A
278Homo sapiensMutation(s): 0 
Gene Names: HLA-C (HLAC)
Find proteins for P04222 (Homo sapiens)
Go to Gene View: HLA-C
Go to UniProtKB:  P04222
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2-MICROGLOBULIN
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE FROM IMPORTIN ALPHA-2
C
9Homo sapiensMutation(s): 0 
Gene Names: KPNA2 (RCH1, SRP1)
Find proteins for P52292 (Homo sapiens)
Go to Gene View: KPNA2
Go to UniProtKB:  P52292
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NATURAL KILLER CELL RECEPTOR KIR2DL2
D, E
200Homo sapiensMutation(s): 0 
Gene Names: KIR2DL2 (CD158B1, NKAT6)
Find proteins for P43627 (Homo sapiens)
Go to Gene View: KIR2DL2
Go to UniProtKB:  P43627
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.540α = 90.00
b = 90.330β = 90.00
c = 207.270γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance