3CII

Structure of NKG2A/CD94 bound to HLA-E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.321 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for NKG2A/CD94 recognition of HLA-E.

Kaiser, B.K.Pizarro, J.C.Kerns, J.Strong, R.K.

(2008) Proc.Natl.Acad.Sci.Usa 105: 6696-6701

  • DOI: 10.1073/pnas.0802736105

  • PubMed Abstract: 
  • The NKG2x/CD94 (x = A, C, E) natural killer-cell receptors perform an important role in immunosurveillance by binding to HLA-E complexes that exclusively present peptides derived from MHC class I leader sequences, thereby monitoring MHC class I expre ...

    The NKG2x/CD94 (x = A, C, E) natural killer-cell receptors perform an important role in immunosurveillance by binding to HLA-E complexes that exclusively present peptides derived from MHC class I leader sequences, thereby monitoring MHC class I expression. We have determined the crystal structure of the NKG2A/CD94/HLA-E complex at 4.4-A resolution, revealing two critical aspects of this interaction. First, the C-terminal region of the peptide, which displays the most variability among class I leader sequences, interacts entirely with CD94, the invariant component of these receptors. Second, residues 167-170 of NKG2A/C account for the approximately 6-fold-higher affinity of the inhibitory NKG2A/CD94 receptor compared to its activating NKG2C/CD94 counterpart. These residues do not contact HLA-E or peptide directly but instead form part of the heterodimer interface with CD94. An evolutionary analysis across primates reveals that whereas CD94 is evolving under purifying selection, both NKG2A and NKG2C are evolving under positive selection. Specifically, residues at the CD94 interface have evolved under positive selection, suggesting that the evolution of these genes is driven by an interaction with pathogen-derived ligands. Consistent with this possibility, we show that NKG2C/CD94, but not NKG2A/CD94, weakly but specifically binds to the CMV MHC-homologue UL18. Thus, the evolution of the NKG2x/CD94 family of receptors has likely been shaped both by the need to bind the invariant HLA-E ligand and the need to avoid subversion by pathogen-derived decoys.


    Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, alpha chain E
A, D
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, E
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
HLA class I histocompatibility antigen peptide
C, F
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
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Natural killer cells antigen CD94
G, I
121Homo sapiensMutation(s): 0 
Gene Names: KLRD1 (CD94)
Find proteins for Q13241 (Homo sapiens)
Go to Gene View: KLRD1
Go to UniProtKB:  Q13241
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NKG2-A/NKG2-B type II integral membrane protein
H, J
120Homo sapiensMutation(s): 0 
Gene Names: KLRC1 (NKG2A)
Find proteins for P26715 (Homo sapiens)
Go to Gene View: KLRC1
Go to UniProtKB:  P26715
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.321 
  • Space Group: I 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 345.983α = 90.00
b = 345.983β = 90.00
c = 345.983γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance