3U83 | pdb_00003u83

Crystal structure of nectin-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.230 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3U83

This is version 1.2 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 37.2 kDa 
  • Atom Count: 2,554 
  • Modeled Residue Count: 300 
  • Deposited Residue Count: 331 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poliovirus receptor-related protein 1331Homo sapiensMutation(s): 0 
Gene Names: PVRL1HVECPRR1
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG6

Query on PG6



Download:Ideal Coordinates CCD File
B [auth A]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.230 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
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
PHASERphasing
PHENIXrefinement
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
  • Version 1.2: 2024-10-09
    Changes: Structure summary