6PAG

Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C.

Moradi, S.Stankovic, S.O'Connor, G.M.Pymm, P.MacLachlan, B.J.Faoro, C.Retiere, C.Sullivan, L.C.Saunders, P.M.Widjaja, J.Cox-Livingstone, S.Rossjohn, J.Brooks, A.G.Vivian, J.P.

(2021) Nat Commun 12: 2173-2173

  • DOI: 10.1038/s41467-021-22359-x
  • Primary Citation of Related Structures:  
    6PA1, 6PAG

  • PubMed Abstract: 
  • The closely related inhibitory killer-cell immunoglobulin-like receptors (KIR), KIR2DL2 and KIR2DL3, regulate the activation of natural killer cells (NK) by interacting with the human leukocyte antigen-C1 (HLA-C1) group of molecules. KIR2DL2, KIR2DL3 and HLA-C1 are highly polymorphic, with this variation being associated with differences in the onset and progression of some human diseases ...

    The closely related inhibitory killer-cell immunoglobulin-like receptors (KIR), KIR2DL2 and KIR2DL3, regulate the activation of natural killer cells (NK) by interacting with the human leukocyte antigen-C1 (HLA-C1) group of molecules. KIR2DL2, KIR2DL3 and HLA-C1 are highly polymorphic, with this variation being associated with differences in the onset and progression of some human diseases. However, the molecular bases underlying these associations remain unresolved. Here, we determined the crystal structures of KIR2DL2 and KIR2DL3 in complex with HLA-C*07:02 presenting a self-epitope. KIR2DL2 differed from KIR2DL3 in docking modality over HLA-C*07:02 that correlates with variabilty of recognition of HLA-C1 allotypes. Mutagenesis assays indicated differences in the mechanism of HLA-C1 allotype recognition by KIR2DL2 and KIR2DL3. Similarly, HLA-C1 allotypes differed markedly in their capacity to inhibit activation of primary NK cells. These functional differences derive, in part, from KIR2DS2 suggesting KIR2DL2 and KIR2DL3 binding geometries combine with other factors to distinguish HLA-C1 functional recognition.


    Organizational Affiliation

    Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia. julian.vivian@monash.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, Cw-7 alpha chainA278Homo sapiensMutation(s): 0 
Gene Names: HLA-CHLAC
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Find proteins for P10321 (Homo sapiens)
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Go to UniProtKB:  P10321
PHAROS:  P10321
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UniProt GroupP10321
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEUC9synthetic constructMutation(s): 0 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Killer cell immunoglobulin-like receptor 2DL3D204Homo sapiensMutation(s): 0 
Gene Names: KIR2DL3CD158B2KIRCL23NKAT2
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Find proteins for P43628 (Homo sapiens)
Explore P43628 
Go to UniProtKB:  P43628
PHAROS:  P43628
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UniProt GroupP43628
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.855α = 90
b = 111.855β = 90
c = 87.994γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references