1MPU

Crystal Structure of the free human NKG2D immunoreceptor

• PDB DOI: https://doi.org/10.2210/pdb1MPU/pdb

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


• Deposited: 2002-09-12 Released: 2003-04-15 
• Deposition Author(s): McFarland, B.J., Kortemme, T., Baker, D., Strong, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.296 
• R-Value Work: 0.245 

Literature

Symmetry Recognizing Asymmetry: Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG2D and MHC Class I-like Ligands

McFarland, B.J., Kortemme, T., Yu, S.F., Baker, D., Strong, R.K.

(2003) Structure 11: 411-422

• PubMed: 12679019 
• DOI: https://doi.org/10.1016/s0969-2126(03)00047-9
• Primary Citation of Related Structures:  
  1MPU


• PubMed Abstract: 
  

  Engagement of diverse protein ligands (MIC-A/B, ULBP, Rae-1, or H60) by NKG2D immunoreceptors mediates elimination of tumorigenic or virally infected cells by natural killer and T cells. Three previous NKG2D-ligand complex structures show the homodimeric receptor interacting with the monomeric ligands in similar 2:1 complexes, with an equivalent surface on each NKG2D monomer binding intimately to a total of six distinct ligand surfaces. Here, the crystal structure of free human NKG2D and in silico and in vitro alanine-scanning mutagenesis analyses of the complex interfaces indicate that NKG2D recognition degeneracy is not explained by a classical induced-fit mechanism. Rather, the divergent ligands appear to utilize different strategies to interact with structurally conserved elements of the consensus NKG2D binding site.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 16.08 kDa 
• Atom Count: 1,171 
• Modelled Residue Count: 128 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NKG2-D type II integral membrane protein	A	138	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P26718 (Homo sapiens) Explore P26718  Go to UniProtKB:  P26718
PHAROS:  P26718 GTEx:  ENSG00000213809

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.296 
• R-Value Work: 0.245 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.65	α = 90
b = 87.65	β = 90
c = 36.13	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-15 
Deposition Author(s): McFarland, B.J., Kortemme, T., Baker, D., Strong, R.K.

Revision History  

• Version 1.0: 2003-04-15
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description