8TM0 | pdb_00008tm0

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

• PDB DOI: https://doi.org/10.2210/pdb8TM0/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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.83 Å
• R-Value Free: 
  0.362 (Depositor) 
• R-Value Work: 
  0.269 (Depositor) 
• R-Value Observed: 
  0.274 (Depositor) 

Starting Model: experimental

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 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.
Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.22 kDa 
• Atom Count: 3,325 
• Modeled Residue Count: 416 
• Deposited Residue Count: 452 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NKG2-D type II integral membrane protein	A	264	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I polypeptide-related sequence A	B [auth C]	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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	2		N/A
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.83 Å
• R-Value Free:  0.362 (Depositor) 
• R-Value Work:  0.269 (Depositor) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.083	α = 90
b = 68.354	β = 90
c = 140.04	γ = 90

Software Package:

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

Structure Validation

Currently 8TM0 does not have a validation slider image.

Entry History 

& Funding Information

Deposition Data

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

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary