3H8N

Crystal Structure Analysis of KIR2DS4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

KIR2DS4 is a product of gene conversion with KIR3DL2 that introduced specificity for HLA-A*11 while diminishing avidity for HLA-C.

Graef, T.Moesta, A.K.Norman, P.J.Abi-Rached, L.Vago, L.Older Aguilar, A.M.Gleimer, M.Hammond, J.A.Guethlein, L.A.Bushnell, D.A.Robinson, P.J.Parham, P.

(2009) J.Exp.Med. 206: 2557-2572

  • DOI: 10.1084/jem.20091010

  • PubMed Abstract: 
  • Human killer cell immunoglobulin-like receptors (KIRs) are distinguished by expansion of activating KIR2DS, whose ligands and functions remain poorly understood. The oldest, most prevalent KIR2DS is KIR2DS4, which is represented by a variable balance ...

    Human killer cell immunoglobulin-like receptors (KIRs) are distinguished by expansion of activating KIR2DS, whose ligands and functions remain poorly understood. The oldest, most prevalent KIR2DS is KIR2DS4, which is represented by a variable balance between "full-length" and "deleted" forms. We find that full-length 2DS4 is a human histocompatibility leukocyte antigen (HLA) class I receptor that binds specifically to subsets of C1+ and C2+ HLA-C and to HLA-A*11, whereas deleted 2DS4 is nonfunctional. Activation of 2DS4+ NKL cells was achieved with A*1102 as ligand, which differs from A*1101 by unique substitution of lysine 19 for glutamate, but not with A*1101 or HLA-C. Distinguishing KIR2DS4 from other KIR2DS is the proline-valine motif at positions 71-72, which is shared with KIR3DL2 and was introduced by gene conversion before separation of the human and chimpanzee lineages. Site-directed swap mutagenesis shows that these two residues are largely responsible for the unique HLA class I specificity of KIR2DS4. Determination of the crystallographic structure of KIR2DS4 shows two major differences from KIR2DL: displacement of contact loop L2 and altered bonding potential because of the substitutions at positions 71 and 72. Correlation between the worldwide distributions of functional KIR2DS4 and HLA-A*11 points to the physiological importance of their mutual interaction.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Killer cell immunoglobulin-like receptor 2DS4
A
195Homo sapiensMutation(s): 0 
Gene Names: KIR2DS4 (CD158I, KKA3, NKAT8)
Find proteins for P43632 (Homo sapiens)
Go to Gene View: KIR2DS4
Go to UniProtKB:  P43632
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.232α = 90.00
b = 62.851β = 90.00
c = 65.934γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
Blu-Icedata collection
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description