Crystal structure of nectin-1

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell adhesion.

Zhang, N.Yan, J.Lu, G.Guo, Z.Fan, Z.Wang, J.Shi, Y.Qi, J.Gao, G.F.

(2011) Nat Commun 2: 577-577

  • DOI: https://doi.org/10.1038/ncomms1571
  • Primary Citation of Related Structures:  
    3U82, 3U83

  • PubMed Abstract: 

    Multiple surface envelope proteins are involved in the human herpes simplex virus type 1 entry and fusion. Among them, glycoprotein D (gD) has an important role by binding to the host receptors such as herpes virus entry mediator and nectin-1. Although the complex structure of gD with herpes virus entry mediator has been established, the binding mode of gD with the nectin-1 is elusive. Nectin-1 is a member of the immunoglobulin (Ig)-like (three Ig-like domains) cell adhesion molecules and is believed to form a homodimer to exert its functions. Here we report the complex structure of gD and nectin-1 (three Ig domains), revealing that gD binds the first Ig domain of nectin-1 in a similar mode to the nectin-1 homodimer interaction. The key amino acids responsible for nectin-1 dimerization are also used for gD/nectin-1 binding. This result indicates that binding of gD to nectin-1 would preclude the nectin-1 dimerization, consequently abolishing its cell adhesion function.

  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beichen West Road, Beijing 100101, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poliovirus receptor-related protein 1331Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15223 (Homo sapiens)
Explore Q15223 
Go to UniProtKB:  Q15223
PHAROS:  Q15223
GTEx:  ENSG00000110400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15223
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PG6

Download Ideal Coordinates CCD File 
C12 H26 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.52α = 90
b = 127.52β = 90
c = 190.555γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description