7DUU

Crystal structure of HLA molecule with an KIR receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Activating receptor KIR2DS2 bound to HLA-C1 reveals the novel recognition features of activating receptor.

Yang, Y.Bai, H.Wu, Y.Chen, P.Zhou, J.Lei, J.Ye, X.Brown, A.J.Zhou, X.Shu, T.Chen, Y.Wei, P.Yin, L.

(2022) Immunology 165: 341-354

  • DOI: https://doi.org/10.1111/imm.13439
  • Primary Citation of Related Structures:  
    7DUU

  • PubMed Abstract: 

    Killer cell immunoglobulin-like receptors (KIRs) are important receptors for regulating the killing of virus-infected or cancer cells of natural killer (NK) cells. KIR2DS2 can recognize peptides derived from hepatitis C virus (HCV) or global flaviviruses (such as dengue and Zika) presented by HLA-C*0102 to activate NK cells, and has shown promising results when used for cancer immunotherapy. Here, we present the complex structure of KIR2DS2 with HLA-C*0102 at a resolution of 2·5Å. Our structure reveals that KIR2DS2 can bind with HLA-C*0102 and HLA-A*1101 in two different directions. Moreover, Tyr45 (in activating receptor KIR2DS2) and Phe45 (in inhibitory KIRs) distinguish the two different binding models and binding affinity between activating KIRs and inhibitory KIRs. The conserved 'AT' motif of the peptide mediates recognition and determines the peptide specificity of recognition. These structural characteristics shed light on how KIRs activate NK cells and can provide a molecular basis for immunotherapy by NK cells.


  • Organizational Affiliation

    State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen273Homo sapiensMutation(s): 0 
Gene Names: HLA-C
UniProt
Find proteins for F6IQA6 (Homo sapiens)
Explore F6IQA6 
Go to UniProtKB:  F6IQA6
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UniProt GroupF6IQA6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LEU-ASN-PRO-SER-VAL-ALA-ALA-THR-LEU9Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
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Go to UniProtKB:  P27958
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UniProt GroupP27958
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Killer cell immunoglobulin-like receptor 2DS2200Homo sapiensMutation(s): 0 
Gene Names: KIR2DS2CD158JNKAT5
UniProt
Find proteins for P43631 (Homo sapiens)
Explore P43631 
Go to UniProtKB:  P43631
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UniProt GroupP43631
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.056α = 90
b = 153.962β = 90
c = 177.556γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description