8X6B

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


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 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


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.Zhang, S.Liu, J.Han, Y.Xiao, J.Chen, Q.Miao, K.Qi, J.Tan, S.Gao, G.F.Wang, H.

(2024) Structure 32: 918-929.e4

  • DOI: https://doi.org/10.1016/j.str.2024.03.012
  • Primary Citation of Related Structures:  
    8X6B

  • PubMed Abstract: 

    Nectin and nectin-like (Necl) co-receptor axis, comprised of receptors DNAM-1, TIGIT, CD96, PVRIG, and nectin/Necl ligands, is gaining prominence in immuno-oncology. Within this axis, the inhibitory receptor PVRIG recognizes Nectin-2 with high affinity, but the underlying molecular basis remains unknown. By determining the crystal structure of PVRIG in complex with Nectin-2, we identified a unique CC' loop in PVRIG, which complements the double-lock-and-key binding mode and contributes to its high affinity for Nectin-2. The association of the corresponding charged residues in the F-strands explains the ligand selectivity of PVRIG toward Nectin-2 but not for Necl-5. Moreover, comprehensive comparisons of the binding capacities between co-receptors and ligands provide innovative insights into the intra-axis immunoregulatory mechanism. Taken together, these findings broaden our understanding of immune recognition and regulation mediated by nectin/Necl co-receptors and provide a rationale for the development of immunotherapeutic strategies targeting the nectin/Necl axis.


  • Organizational Affiliation

    Institutes of Physical Science and Information Technology, Anhui University, Anhui 230601, China; Cancer Center, Faculty of Health Sciences, University of Macau, Taipa Macau SAR, China; Beijing Life Science Academy, Beijing 102200, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein PVRIGA [auth B]141Homo sapiensMutation(s): 1 
Gene Names: PVRIGC7orf15
UniProt & NIH Common Fund Data Resources
Find proteins for Q6DKI7 (Homo sapiens)
Explore Q6DKI7 
Go to UniProtKB:  Q6DKI7
GTEx:  ENSG00000213413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DKI7
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q6DKI7-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nectin-2B [auth A]128Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92692
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
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 = 80.974α = 90
b = 80.974β = 90
c = 82.742γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references
  • Version 1.2: 2024-07-24
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Structure summary