3WYR

Crystal structure of Killer cell immunoglobulin-like receptor 2DL4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of the atypical killer cell immunoglobulin-like receptor, KIR2DL4.

Moradi, S.Berry, R.Pymm, P.Hitchen, C.Beckham, S.A.Wilce, M.C.Walpole, N.G.Clements, C.S.Reid, H.H.Perugini, M.A.Brooks, A.G.Rossjohn, J.Vivian, J.P.

(2015) J.Biol.Chem. 290: 10460-10471

  • DOI: 10.1074/jbc.M114.612291

  • PubMed Abstract: 
  • The engagement of natural killer cell immunoglobulin-like receptors (KIRs) with their target ligands, human leukocyte antigen (HLA) molecules, is a critical component of innate immunity. Structurally, KIRs typically have either two (D1-D2) or three ( ...

    The engagement of natural killer cell immunoglobulin-like receptors (KIRs) with their target ligands, human leukocyte antigen (HLA) molecules, is a critical component of innate immunity. Structurally, KIRs typically have either two (D1-D2) or three (D0-D1-D2) extracellular immunoglobulin domains, with the D1 and D2 domain recognizing the α1 and α2 helices of HLA, respectively, whereas the D0 domain of the KIR3DLs binds a loop region flanking the α1 helix of the HLA molecule. KIR2DL4 is distinct from other KIRs (except KIR2DL5) in that it does not contain a D1 domain and instead has a D0-D2 arrangement. Functionally, KIR2DL4 is also atypical in that, unlike all other KIRs, KIR2DL4 has both activating and inhibitory signaling domains. Here, we determined the 2.8 Å crystal structure of the extracellular domains of KIR2DL4. Structurally, KIR2DL4 is reminiscent of other KIR2DL receptors, with the D0 and D2 adopting the C2-type immunoglobulin fold arranged with an acute elbow angle. However, KIR2DL4 self-associated via the D0 domain in a concentration-dependent manner and was observed as a tetramer in the crystal lattice by size exclusion chromatography, dynamic light scattering, analytical ultracentrifugation, and small angle x-ray scattering experiments. The assignment of residues in the D0 domain to forming the KIR2DL4 tetramer precludes an interaction with HLA akin to that observed for KIR3DL1. Accordingly, no interaction was observed to HLA by direct binding studies. Our data suggest that the unique functional properties of KIR2DL4 may be mediated by self-association of the receptor.


    Organizational Affiliation

    the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne Victoria 3086 Australia.,From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,the Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia, and.,From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and.,From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, Julian.vivian@monash.edu.,From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, the Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom Jamie.rossjohn@monash.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Killer cell immunoglobulin-like receptor 2DL4
A, B
206Homo sapiensMutation(s): 0 
Gene Names: KIR2DL4 (CD158D, KIR103AS)
Find proteins for Q99706 (Homo sapiens)
Go to Gene View: KIR2DL4
Go to UniProtKB:  Q99706
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.836α = 90.00
b = 87.836β = 90.00
c = 105.996γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
Blu-Icedata collection
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2020-01-01
    Type: Database references, Derived calculations