8TLZ

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

• PDB DOI: https://doi.org/10.2210/pdb8TLZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-07-27 Released: 2024-04-17 
• Deposition Author(s): Rupert, P.B., Strong, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 

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

• PubMed: 38586421 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I polypeptide-related sequence A	A, B	188	Homo sapiens	Mutation(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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
LMR	E [auth A], H [auth B]	(2S)-2-hydroxybutanedioic acid C4 H6 O5 BJEPYKJPYRNKOW-REOHCLBHSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.823	α = 90
b = 127.823	β = 90
c = 157.017	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Rupert, P.B., Strong, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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