3VH8

KIR3DL1 in complex with HLA-B*5701


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nature10517

  • 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 pivota ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-57 alpha chain
A, D
275Homo sapiensGene Names: HLA-B (HLAB)
Find proteins for P18465 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P18465
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
99Homo sapiensGene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptide of Ig kappa chain C region
C, F
9Homo sapiensGene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Go to UniProtKB:  P01834
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Killer cell immunoglobulin-like receptor 3DL1
G, H
316Homo sapiensGene Names: KIR3DL1 (CD158E, NKAT3, NKB1)
Find proteins for P43629 (Homo sapiens)
Go to Gene View: KIR3DL1
Go to UniProtKB:  P43629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • 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
REFMACrefinement
SCALAdata scaling
Blu-Icedata collection
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-12-07
    Type: Database references