3ALP

Cell adhesion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the cis-Dimer of Nectin-1: implications for the architecture of cell-cell junctions

Narita, H.Yamamoto, Y.Suzuki, M.Miyazaki, N.Yoshida, A.Kawai, K.Iwasaki, K.Nakagawa, A.Takai, Y.Sakisaka, T.

(2011) J.Biol.Chem. 286: 12659-12669

  • DOI: 10.1074/jbc.M110.197368

  • PubMed Abstract: 
  • In multicellular organisms, cells are interconnected by cell adhesion molecules. Nectins are immunoglobulin (Ig)-like cell adhesion molecules that mediate homotypic and heterotypic cell-cell adhesion, playing key roles in tissue organization. To medi ...

    In multicellular organisms, cells are interconnected by cell adhesion molecules. Nectins are immunoglobulin (Ig)-like cell adhesion molecules that mediate homotypic and heterotypic cell-cell adhesion, playing key roles in tissue organization. To mediate cell-cell adhesion, nectin molecules dimerize in cis on the surface of the same cell, followed by trans-dimerization of the cis-dimers between the neighboring cells. Previous cell biological studies deduced that the first Ig-like domain of nectin and the second Ig-like domain are involved in trans-dimerization and cis-dimerization, respectively. However, to understand better the steps involved in nectin adhesion, the structural basis for the dimerization of nectin must be determined. In this study, we determined the first crystal structure of the entire extracellular region of nectin-1. In the crystal, nectin-1 formed a V-shaped homophilic dimer through the first Ig-like domain. Structure-based site-directed mutagenesis of the first Ig-like domain identified four essential residues that are involved in the homophilic dimerization. Upon mutating the four residues, nectin-1 significantly decreased cis-dimerization on the surface of cultured cells and abolished the homophilic and heterophilic adhesion activities. These results indicate that, in contrast with the previous notion, our structure represents a cis-dimer. Thus, our findings clearly reveal the structural basis for the cis-dimerization of nectins through the first Ig-like domains.


    Organizational Affiliation

    Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Suita 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poliovirus receptor-related protein 1
A, B
331Homo sapiensMutation(s): 0 
Gene Names: NECTIN1 (HVEC, PRR1, PVRL1)
Find proteins for Q15223 (Homo sapiens)
Go to Gene View: NECTIN1
Go to UniProtKB:  Q15223
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download SDF File 
Download CCD File 
B
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 164.924α = 90.00
b = 164.924β = 90.00
c = 164.924γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL2Mapmodel building
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
HKL2Mapphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-08-07
    Type: Database references
  • Version 1.3: 2017-10-11
    Type: Refinement description