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 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NKG2-D type II integral membrane protein264Homo sapiensMutation(s): 0 
Gene Names: KLRK1D12S2489ENKG2D
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
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P26718-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (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
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q29983-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

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
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

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
  • Version 1.1: 2024-11-13
    Changes: Structure summary