3CDG

Human CD94/NKG2A in complex with HLA-E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence

Petrie, E.J.Clements, C.S.Lin, J.Sullivan, L.C.Johnson, D.Huyton, T.Heroux, A.Hoare, H.L.Beddoe, T.Reid, H.H.Wilce, M.C.J.Brooks, A.G.Rossjohn, J.

(2008) J.Exp.Med. 205: 725-735

  • DOI: 10.1084/jem.20072525

  • PubMed Abstract: 
  • The recognition of human leukocyte antigen (HLA)-E by the heterodimeric CD94-NKG2 natural killer (NK) receptor family is a central innate mechanism by which NK cells monitor the expression of other HLA molecules, yet the structural basis of this high ...

    The recognition of human leukocyte antigen (HLA)-E by the heterodimeric CD94-NKG2 natural killer (NK) receptor family is a central innate mechanism by which NK cells monitor the expression of other HLA molecules, yet the structural basis of this highly specific interaction is unclear. Here, we describe the crystal structure of CD94-NKG2A in complex with HLA-E bound to a peptide derived from the leader sequence of HLA-G. The CD94 subunit dominated the interaction with HLA-E, whereas the NKG2A subunit was more peripheral to the interface. Moreover, the invariant CD94 subunit dominated the peptide-mediated contacts, albeit with poor surface and chemical complementarity. This unusual binding mode was consistent with mutagenesis data at the CD94-NKG2A-HLA-E interface. There were few conformational changes in either CD94-NKG2A or HLA-E upon ligation, and such a "lock and key" interaction is typical of innate receptor-ligand interactions. Nevertheless, the structure also provided insight into how this interaction can be modulated by subtle changes in the peptide ligand or by the pairing of CD94 with other members of the NKG2 family. Differences in the docking strategies used by the NKG2D and CD94-NKG2A receptors provided a basis for understanding the promiscuous nature of ligand recognition by NKG2D compared with the fidelity of the CD94-NKG2 receptors.


    Organizational Affiliation

    The Protein Crystallography Unit, ARC Centre of Excellence in Structural and Functional Microbial Genomics, 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, alpha chain E
A, C
273Homo sapiensMutation(s): 0 
Gene Names: HLA-E (HLA-6.2, HLAE)
Find proteins for P13747 (Homo sapiens)
Go to Gene View: HLA-E
Go to UniProtKB:  P13747
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Natural killer cells antigen CD94
J, E
123Homo sapiensMutation(s): 0 
Gene Names: KLRD1 (CD94)
Find proteins for Q13241 (Homo sapiens)
Go to Gene View: KLRD1
Go to UniProtKB:  Q13241
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NKG2-A/NKG2-B type II integral membrane protein
K, F
120Homo sapiensMutation(s): 0 
Gene Names: KLRC1 (NKG2A)
Find proteins for P26715 (Homo sapiens)
Go to Gene View: KLRC1
Go to UniProtKB:  P26715
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
leader peptide of HLA class I histocompatibility antigen, alpha chain G
P, Q
9Homo sapiensMutation(s): 0 
Gene Names: HLA-G (HLA-6.0, HLAG)
Find proteins for P17693 (Homo sapiens)
Go to Gene View: HLA-G
Go to UniProtKB:  P17693
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 
  • Space Group: I 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 345.201α = 90.00
b = 345.201β = 90.00
c = 345.201γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
ADSCdata collection
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance