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: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.209 

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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
  • Primary Citation of Related Structures:  
    1EFX

  • 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 U S A 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA-CW3 (HEAVY CHAIN)A278Homo sapiensMutation(s): 0 
Gene Names: HLA-C, HLAC
Find proteins for P10321 (Homo sapiens)
Explore P10321 
Go to UniProtKB:  P10321
NIH Common Fund Data Resources
PHAROS  P10321
GTEx  ENSG00000204525
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-2-MICROGLOBULINB100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
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PHAROS  P61769
GTEx  ENSG00000166710
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE FROM IMPORTIN ALPHA-2C9N/AMutation(s): 0 
Find proteins for P52292 (Homo sapiens)
Explore P52292 
Go to UniProtKB:  P52292
NIH Common Fund Data Resources
PHAROS  P52292
GTEx  ENSG00000182481
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NATURAL KILLER CELL RECEPTOR KIR2DL2D, E200Homo sapiensMutation(s): 0 
Gene Names: KIR2DL2, CD158B1, NKAT6
Find proteins for P43627 (Homo sapiens)
Explore P43627 
Go to UniProtKB:  P43627
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.54α = 90
b = 90.33β = 90
c = 207.27γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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