3R0N

Crystal Structure of the Immunoglobulin variable domain of Nectin-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure of Nectin-2 reveals determinants of homophilic and heterophilic interactions that control cell-cell adhesion.

Samanta, D.Ramagopal, U.A.Rubinstein, R.Vigdorovich, V.Nathenson, S.G.Almo, S.C.

(2012) Proc.Natl.Acad.Sci.USA 109: 14836-14840

  • DOI: 10.1073/pnas.1212912109

  • PubMed Abstract: 
  • Nectins are members of the Ig superfamily that mediate cell-cell adhesion through homophilic and heterophilic interactions. We have determined the crystal structure of the nectin-2 homodimer at 1.3 Å resolution. Structural analysis and complementary ...

    Nectins are members of the Ig superfamily that mediate cell-cell adhesion through homophilic and heterophilic interactions. We have determined the crystal structure of the nectin-2 homodimer at 1.3 Å resolution. Structural analysis and complementary mutagenesis studies reveal the basis for recognition and selectivity among the nectin family members. Notably, the close proximity of charged residues at the dimer interface is a major determinant of the binding affinities associated with homophilic and heterophilic interactions within the nectin family. Our structural and biochemical data provide a mechanistic basis to explain stronger heterophilic versus weaker homophilic interactions among these family members and also offer insights into nectin-mediated transinteractions between engaging cells.


    Organizational Affiliation

    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poliovirus receptor-related protein 2
A
128Homo sapiensMutation(s): 0 
Gene Names: NECTIN2 (HVEB, PRR2, PVRL2)
Find proteins for Q92692 (Homo sapiens)
Go to Gene View: NECTIN2
Go to UniProtKB:  Q92692
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.964α = 90.00
b = 57.964β = 90.00
c = 67.544γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-09-05
    Type: Database references
  • Version 1.3: 2012-09-12
    Type: Structure summary
  • Version 1.4: 2012-10-03
    Type: Database references
  • Version 1.5: 2012-11-07
    Type: Data collection