8TLZ | pdb_00008tlz

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.270 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.230 (Depositor) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 46.04 kDa 
  • Atom Count: 2,810 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 376 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I polypeptide-related sequence A
A, B
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: 2
Go to GlyGen: Q29983-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.270 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.230 (Depositor) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.823α = 90
b = 127.823β = 90
c = 157.017γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

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