8X6B

Crystal structure of immune receptor PVRIG in complex with ligand Nectin-2

• PDB DOI: https://doi.org/10.2210/pdb8X6B/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Baculovirus transfer vector pFASTBAC1, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-21 Released: 2024-04-24 
• Deposition Author(s): Hu, S.T., Han, P., Wang, H., Qi, J.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Structural basis for the immune recognition and selectivity of the immune receptor PVRIG for ligand Nectin-2

Hu, S., Han, P., Wang, M., Cao, X., Liu, H., Zhang, S., Liu, W.J., Han, Y., Xiao, J., Chen, Q., Miao, K., Qi, J., Tan, S., Wang, H., Gao, G.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 28.77 kDa 
• Atom Count: 1,872 
• Modelled Residue Count: 229 
• Deposited Residue Count: 269 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein PVRIG	A [auth B]	141	Homo sapiens	Mutation(s): 1  Gene Names: PVRIG, C7orf15
UniProt & NIH Common Fund Data Resources
Find proteins for Q6DKI7 (Homo sapiens) Explore Q6DKI7  Go to UniProtKB:  Q6DKI7
GTEx:  ENSG00000213413

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nectin-2	B [auth A]	128	Homo sapiens	Mutation(s): 0  Gene Names: NECTIN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92692 (Homo sapiens) Explore Q92692  Go to UniProtKB:  Q92692
PHAROS:  Q92692 GTEx:  ENSG00000130202

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.974	α = 90
b = 80.974	β = 90
c = 82.742	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Hu, S.T., Han, P., Wang, H., Qi, J.X.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release