Interactive structural biology · Open data

NKG2D recognition complex — 3D molecular viewer

Interactive 3D structure of the human NKG2D extracellular domain bound to MICA — the published crystallographic basis for the recognition module of the NKG2D-LIF6 chimera. Rotate, zoom, switch representations in any modern browser. WebXR-capable browsers (Quest, Vision Pro Safari, AR-capable mobile Chrome) can launch the viewer in AR/VR via the button below; the WebXR session uses standard NGL viewer XR support.

Reference structure: PDB 1HYR — Crystal structure of the human NKG2D-MICA complex (Li et al. 2001, Nature Immunology)
Source: RCSB Protein Data Bank (CC0 public domain, NCBI)
Resolution: 2.7 Å
Components shown: NKG2D extracellular domain (chain A) · MICA α1+α2 platform (chain B)
Relevance to Nightbox: The NKG2D extracellular domain shown here (residues 79-216) is the recognition module of the NKG2D-LIF6 chimera (NBX-001). The MICA ligand shown here is the tumor-restricted stress signal the chimera responds to.

Reading the structure

NKG2D ECD (chain A): the C-type lectin-like fold that recognizes MICA. This is the residue range (79-216) used in the chimeric construct.
MICA (chain B): stress-induced ligand expressed selectively on transformed and stressed cells — the tumor-restricted signal the chimera responds to.
The interface: NKG2D engages MICA's α1-α2 platform via a specific contact surface. The published crystallographic interface guides the chimera's selectivity argument.

What is NOT shown here

The chimera fusion construct itself — no published crystal structure exists yet (in silico design only)
The elephant LIF6 effector domain — modeled by AlphaFold3; full 3D rendering will be released alongside the wet-lab validation data Q3-Q4 2026
The mitochondrial localization context

Open methodology

The structural validation pipeline (AlphaFold3 + RoseTTAFold all-atom + PyMOL + Rosetta refinement) for the NKG2D-LIF6 chimera is documented at github.com/nightbox-llc/chimera-design-notes/METHODS.md under CC BY 4.0.

Use this viewer in your own work

The viewer is open-source — pulls PDB files directly from the RCSB CDN, uses the NGL viewer JS library (MIT license), and is fully embeddable. Right-click → "Inspect" to see the implementation. Or fork at github.com/nightbox-llc/nightbox-website.

PDB structures shown are public domain (CC0) per RCSB Protein Data Bank policy. Molecular visualization powered by NGL Viewer (MIT license, Rose et al. 2018).