8TM2

Preclinical Characterization of Pan-NKG2D Ligand-Binding NKG2D Receptor Decoys

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Literature

Preclinical characterization of Pan-NKG2D ligand-binding NKG2D receptor decoys.

Rupert, P.B., Buerger, M., Girard, E.J., Frutoso, M., Parrilla, D., Ng, K., Gooley, T., Groh, V., Strong, R.K.

(2024) Heliyon 10: e28583-e28583

  • DOI: https://doi.org/10.1016/j.heliyon.2024.e28583
  • Primary Citation of Related Structures:  
    8TLZ, 8TM0, 8TM2

  • PubMed Abstract: 

    NKG2D and its ligands are critical regulators of protective immune responses controlling infections and cancer, defining a crucial immune signaling axis. Current therapeutic efforts targeting this axis almost exclusively aim at enhancing NKG2D-mediated effector functions. However, this axis can drive disease processes when dysregulated, in particular, driving stem-like cancer cell reprogramming and tumorigenesis through receptor/ligand self-stimulation on tumor cells. Despite complexities with its structure and biology, we developed multiple novel engineered proteins that functionally serve as axis-blocking NKG2D "decoys" and report biochemical, structural, in vitro , and in vivo evaluation of their functionality.

    • Organizational Affiliation: 

    Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NKG2-D type II integral membrane protein264Homo sapiensMutation(s): 0 
Gene Names: KLRK1, D12S2489E, NKG2D
UniProt & NIH Common Fund Data Resources
Find proteins for P26718 (Homo sapiens)
Explore P26718 
Go to UniProtKB:  P26718
PHAROS:  P26718
GTEx:  ENSG00000213809 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26718
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I polypeptide-related sequence AB [auth C]188Homo sapiensMutation(s): 0 
Gene Names: MICA
UniProt & NIH Common Fund Data Resources
Find proteins for Q29983 (Homo sapiens)
Explore Q29983 
Go to UniProtKB:  Q29983
PHAROS:  Q29983
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ29983
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth D],
D [auth B]		2N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.571α = 90
b = 69.782β = 90
c = 145.374γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release