4PP8

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

• PDB DOI: https://doi.org/10.2210/pdb4PP8/pdb
• Entry: 4PP8 supersedes: 1JSK

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-02-26 Released: 2014-04-09 
• Deposition Author(s): Li, P., Strong, R.K.

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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 

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

• PubMed: 11825567 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.93 kDa 
• Atom Count: 4,534 
• Modelled Residue Count: 546 
• Deposited Residue Count: 598 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NKG2-D type II integral membrane protein	A, B	125	Mus musculus	Mutation(s): 0  Gene Names: Klrk1, Nkg2d, RAE-1 BETA
UniProt & NIH Common Fund Data Resources
Find proteins for O54709 (Mus musculus) Explore O54709  Go to UniProtKB:  O54709
IMPC:  MGI:1196250

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid early-inducible protein 1-beta	C, D	174	Mus musculus	Mutation(s): 0  Gene Names: NKG2D, Raet1b
UniProt
Find proteins for O08603 (Mus musculus) Explore O08603  Go to UniProtKB:  O08603

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 58.637	α = 90
b = 58.637	β = 90
c = 350.33	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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