4PP8

Crystal structure of murine NK cell ligand RAE-1 beta in complex with NKG2D

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Crystal structures of RAE-1beta and its complex with the activating immunoreceptor NKG2D.

Li, P., McDermott, G., Strong, R.K.

(2002) Immunity 16: 77-86

  • DOI: 10.1016/s1074-7613(02)00258-3
  • Primary Citation of Related Structures:  
    1JFM, 4PP8

  • PubMed Abstract: 

    • Induced by retinoic acid and implicated in playing a role in development, rodent RAE-1 proteins are ligands for the activating immunoreceptor NKG2D, widely expressed on natural killer cells, T cells, and macrophages. RAE-1 proteins (alpha, beta, gamma, and delta) are distant major histocompatibility complex (MHC) class I homologs, comprising isolated alpha1alpha2 platform domains ...

    Induced by retinoic acid and implicated in playing a role in development, rodent RAE-1 proteins are ligands for the activating immunoreceptor NKG2D, widely expressed on natural killer cells, T cells, and macrophages. RAE-1 proteins (alpha, beta, gamma, and delta) are distant major histocompatibility complex (MHC) class I homologs, comprising isolated alpha1alpha2 platform domains. The crystal structure of RAE-1beta was distorted from other MHC homologs and displayed noncanonical disulfide bonds. The loss of any remnant of a peptide binding groove was facilitated by the close approach of the groove-defining helices through a hydrophobic, leucine-rich interface. The RAE-1beta-murine NKG2D complex structure resembled the human NKG2D-MICA receptor-ligand complex and further demonstrated the promiscuity of the NKG2D ligand binding site.

    Related Citations: 
    • Retinoic acid early inducible genes define a ligand family for the activating NKG2D receptor in mice.
      Cerwenka, A., Bakker, A.B., McClanahan, T., Wagner, J., Wu, J., Phillips, J.H., Lanier, L.L.
      (2000) Immunity 12: 721
    • Ligands for the murine NKG2D receptor: expression by tumor cells and activation of NK cells and macrophages.
      Diefenbach, A., Jamieson, A.M., Liu, S.D., Shastri, N., Raulet, D.H.
      (2000) Nat Immunol 1: 119
    Organizational Affiliation: 

    Fred Hutchinson Cancer Research Center, Division of Basic Sciences, Seattle, WA 98109, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NKG2-D type II integral membrane proteinA, B125Mus musculusMutation(s): 0 
Gene Names: Klrk1, Nkg2d, RAE-1 BETA
UniProt
Find proteins for O54709 (Mus musculus)
Explore O54709 
Go to UniProtKB:  O54709
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO54709
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid early-inducible protein 1-betaC, D174Mus musculusMutation(s): 0 
Gene Names: NKG2D, Raet1b
UniProt
Find proteins for O08603 (Mus musculus)
Explore O08603 
Go to UniProtKB:  O08603
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08603
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.637α = 90
b = 58.637β = 90
c = 350.33γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2014-02-26 
  • Released Date: 2014-04-09 
    • Deposition Author(s): Li, P., Strong, R.K.
  • This entry supersedes: 1JSK

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release