4N8V

Crystal structure of killer cell immunoglobulin-like receptor KIR2DS2 in complex with HLA-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Activating killer cell immunoglobulin-like receptor 2DS2 binds to HLA-A*11

Liu, J.X.Xiao, Z.W.Ko, H.L.Shen, M.X.Ren, E.C.

(2014) Proc.Natl.Acad.Sci.USA 111: 2662-2667

  • DOI: 10.1073/pnas.1322052111

  • PubMed Abstract: 
  • Inhibitory killer cell Ig-like receptors (KIRs) are known to recognize HLA ligands mainly of the HLA-C and Bw4 groups, but the ligands for KIRs are poorly understood. We report here the identification of the cognate ligand for the activating KIR 2DS2 ...

    Inhibitory killer cell Ig-like receptors (KIRs) are known to recognize HLA ligands mainly of the HLA-C and Bw4 groups, but the ligands for KIRs are poorly understood. We report here the identification of the cognate ligand for the activating KIR 2DS2 as HLA-A*11:01. The crystal structure of the KIR2DS2-HLA-A*11:01 complex was solved at 2.5-Å resolution and revealed residue-binding characteristics distinct from those of inhibitory KIRs with HLA-C and the critical role of residues Tyr45 and Asp72 in shaping binding specificity to HLA-A*11:01. Using KIR2DS2 tetramers, binding to surface HLA-A*11:01 on live cells was demonstrated and, furthermore, that binding can be altered by residue changes at p8 of the peptide, indicating the influence of peptide sequence on KIR-HLA association. In addition, heteronuclear single quantum coherence NMR was used to map the involvement of critical residues in HLA binding at the interface of KIR and HLA, and validates the data observed in the crystal structure. Our data provide structural evidence of the recognition of A*11:01 by the activating KIR2DS2 and extend our understanding of the KIR-HLA binding spectrum.


    Organizational Affiliation

    Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Killer cell immunoglobulin-like receptor 2DS2
G, I
201Homo sapiensMutation(s): 0 
Gene Names: KIR2DS2 (CD158J, NKAT5)
Find proteins for P43631 (Homo sapiens)
Go to Gene View: KIR2DS2
Go to UniProtKB:  P43631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-11 alpha chain
A, D
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P13746 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P13746
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
peptide from Virion membrane protein A14
C, F
9Vaccinia virus (strain Western Reserve)Mutation(s): 0 
Gene Names: VACWR133
Find proteins for Q76ZQ3 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  Q76ZQ3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.550α = 90.00
b = 94.670β = 90.00
c = 228.440γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data collection
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-18 
  • Released Date: 2014-02-05 
  • Deposition Author(s): Liu, J.X., Ren, E.C.

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references
  • Version 1.2: 2014-03-12
    Type: Database references