3CDG

Human CD94/NKG2A in complex with HLA-E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

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
  • Primary Citation of Related Structures:  
    3CDG

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, alpha chain EAC273Homo sapiensMutation(s): 0 
Gene Names: HLA-EHLA-6.2HLAE
Find proteins for P13747 (Homo sapiens)
Explore P13747 
Go to UniProtKB:  P13747
NIH Common Fund Data Resources
PHAROS  P13747
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBD100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Natural killer cells antigen CD94EJ123Homo sapiensMutation(s): 0 
Gene Names: KLRD1CD94
Find proteins for Q13241 (Homo sapiens)
Explore Q13241 
Go to UniProtKB:  Q13241
NIH Common Fund Data Resources
PHAROS  Q13241
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NKG2-A/NKG2-B type II integral membrane proteinFK120Homo sapiensMutation(s): 0 
Gene Names: KLRC1NKG2A
Find proteins for P26715 (Homo sapiens)
Explore P26715 
Go to UniProtKB:  P26715
NIH Common Fund Data Resources
PHAROS  P26715
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
leader peptide of HLA class I histocompatibility antigen, alpha chain GPQ9N/AMutation(s): 0 
Find proteins for P17693 (Homo sapiens)
Explore P17693 
Go to UniProtKB:  P17693
NIH Common Fund Data Resources
PHAROS  P17693
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 345.201α = 90
b = 345.201β = 90
c = 345.201γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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