3R0N

Crystal Structure of the Immunoglobulin variable domain of Nectin-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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 U S A 109: 14836-14840

  • DOI: 10.1073/pnas.1212912109
  • Primary Citation of Related Structures:  
    3R0N

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poliovirus receptor-related protein 2A128Homo sapiensMutation(s): 0 
Gene Names: HVEBPRR2PVRL2NECTIN2
Find proteins for Q92692 (Homo sapiens)
Explore Q92692 
Go to UniProtKB:  Q92692
NIH Common Fund Data Resources
PHAROS  Q92692
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.964α = 90
b = 57.964β = 90
c = 67.544γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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