3VH8

KIR3DL1 in complex with HLA-B*5701


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B

Vivian, J.P.Duncan, R.C.Berry, R.O'Connor, G.M.Reid, H.H.Beddoe, T.Gras, S.Saunders, P.M.Olshina, M.A.Widjaja, J.M.L.Harpur, C.M.Lin, J.Maloveste, S.M.Price, D.A.Lafont, B.A.P.McVicar, D.W.Clements, C.S.Brooks, A.G.Rossjohn, J.

(2011) Nature 479: 401-405

  • DOI: https://doi.org/10.1038/nature10517
  • Primary Citation of Related Structures:  
    3VH8

  • PubMed Abstract: 

    Members of the killer cell immunoglobulin-like receptor (KIR) family, a large group of polymorphic receptors expressed on natural killer (NK) cells, recognize particular peptide-laden human leukocyte antigen (pHLA) class I molecules and have a pivotal role in innate immune responses. Allelic variation and extensive polymorphism within the three-domain KIR family (KIR3D, domains D0-D1-D2) affects pHLA binding specificity and is linked to the control of viral replication and the treatment outcome of certain haematological malignancies. Here we describe the structure of a human KIR3DL1 receptor bound to HLA-B*5701 complexed with a self-peptide. KIR3DL1 clamped around the carboxy-terminal end of the HLA-B*5701 antigen-binding cleft, resulting in two discontinuous footprints on the pHLA. First, the D0 domain, a distinguishing feature of the KIR3D family, extended towards β2-microglobulin and abutted a region of the HLA molecule with limited polymorphism, thereby acting as an 'innate HLA sensor' domain. Second, whereas the D2-HLA-B*5701 interface exhibited a high degree of complementarity, the D1-pHLA-B*5701 contacts were suboptimal and accommodated a degree of sequence variation both within the peptide and the polymorphic region of the HLA molecule. Although the two-domain KIR (KIR2D) and KIR3DL1 docked similarly onto HLA-C and HLA-B respectively, the corresponding D1-mediated interactions differed markedly, thereby providing insight into the specificity of KIR3DL1 for discrete HLA-A and HLA-B allotypes. Collectively, in association with extensive mutagenesis studies at the KIR3DL1-pHLA-B*5701 interface, we provide a framework for understanding the intricate interplay between peptide variability, KIR3D and HLA polymorphism in determining the specificity requirements of this essential innate interaction that is conserved across primate species.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-57 alpha chainA,
E [auth D]
275Homo sapiensMutation(s): 0 
Gene Names: HLA-B*5701
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
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Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinB,
F [auth E]
99Homo 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
peptide of Ig kappa chain C regionC,
G [auth F]
9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
Entity Groups  
UniProt GroupP01834
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Killer cell immunoglobulin-like receptor 3DL1D [auth G],
H
316Homo sapiensMutation(s): 0 
Gene Names: KIR3DL1*001
UniProt & NIH Common Fund Data Resources
Find proteins for P43629 (Homo sapiens)
Explore P43629 
Go to UniProtKB:  P43629
PHAROS:  P43629
GTEx:  ENSG00000167633 
Entity Groups  
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UniProt GroupP43629
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P43629-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.248α = 100.56
b = 66.374β = 92.83
c = 93.361γ = 101.56
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary