9DH2 image
Deposition Date 2024-09-03
Release Date 2024-12-04
Last Version Date 2024-12-18
Entry Detail
PDB ID:
9DH2
Keywords:
Title:
Structure of Fab in complex with NKG2D extracellular domain
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.98 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Fab heavy chain
Chain IDs:A, C (auth: G), E (auth: K), H (auth: P)
Chain Length:220
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Fab light chain
Chain IDs:B (auth: D), D (auth: H), F (auth: L), I (auth: Q)
Chain Length:212
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:NKG2-D type II integral membrane protein
Gene (Uniprot):KLRK1
Chain IDs:G (auth: M), J (auth: R), K (auth: S), L (auth: T)
Chain Length:137
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Agonistic anti-NKG2D antibody structure reveals unique stoichiometry and epitope compared to natural ligands.
Mabs 16 2433121 2433121 (2024)
PMID: 39582357 DOI: 10.1080/19420862.2024.2433121

Abstact

Natural killer (NK) cells are effector cells of the innate immune system that distinguish between healthy and abnormal cells through activating and inhibitory receptor signaling. NKG2D, a homodimeric activating receptor expressed on NK cells, recognizes a diverse class of stress ligands expressed by cells experiencing infection, malignant transformation, chronic inflammation, and other cellular stresses. Despite the variety of NKG2D ligands, they all bind the receptor asymmetrically in a 1:1 ligand to homodimeric NKG2D stoichiometry. In contrast, as we report herein, the agonistic antibody 2D3 binds NKG2D with a 2:1 stoichiometry of its antigen binding fragments to homodimeric NKG2D and a largely distinct epitope. This binding interaction, as compared to NKG2D natural ligands, suggests there may be unique mechanisms to engage this receptor while offering possible benefits when incorporated into an IgG-based therapeutic.

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Primary Citation of related structures