1KCG

NKG2D in complex with ULBP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational plasticity revealed by the cocrystal structure of NKG2D and its class I MHC-like ligand ULBP3.

Radaev, S.Rostro, B.Brooks, A.G.Colonna, M.Sun, P.D.

(2001) Immunity 15: 1039-1049


  • PubMed Abstract: 
  • NKG2D is known to trigger the natural killer (NK) cell lysis of various tumor and virally infected cells. In the NKG2D/ULBP3 complex, the structure of ULBP3 resembles the alpha1 and alpha2 domains of classical MHC molecules without a bound peptide. T ...

    NKG2D is known to trigger the natural killer (NK) cell lysis of various tumor and virally infected cells. In the NKG2D/ULBP3 complex, the structure of ULBP3 resembles the alpha1 and alpha2 domains of classical MHC molecules without a bound peptide. The lack of alpha3 and beta2m domains is compensated by replacing two hydrophobic patches at the underside of the class I MHC-like beta sheet floor with a group of hydrophilic and charged residues in ULBP3. NKG2D binds diagonally across the ULBP3 alpha helices, creating a complementary interface, an asymmetrical subunit orientation, and local conformational adjustments in the receptor. The interface is stabilized primarily by hydrogen bonds and hydrophobic interactions. Unlike the KIR receptors that recognize a conserved HLA region by a lock-and-key mechanism, NKG2D recognizes diverse ligands by an induced-fit mechanism.


    Organizational Affiliation

    Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, MD 20852, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NKG2-D type II integral membrane protein
A, B
124Homo sapiensGene Names: KLRK1 (D12S2489E, NKG2D)
Find proteins for P26718 (Homo sapiens)
Go to Gene View: KLRK1
Go to UniProtKB:  P26718
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ULBP3 protein
C
178Homo sapiensGene Names: ULBP3 (N2DL3, RAET1N)
Find proteins for Q9BZM4 (Homo sapiens)
Go to Gene View: ULBP3
Go to UniProtKB:  Q9BZM4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download SDF File 
Download CCD File 
C
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.050α = 90.00
b = 62.050β = 90.00
c = 237.310γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
MARdata collection
MARdata reduction
SOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-11-08 
  • Released Date: 2002-01-09 
  • Deposition Author(s): Radaev, S., Sun, P.

Revision History 

  • Version 1.0: 2002-01-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance