Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14010.54 
• Atom Count: 1106 
• Residue Count: 128 
• Unique protein chains: 1

3R0N

Crystal Structure of the Immunoglobulin variable domain of Nectin-2

• DOI: 10.2210/pdb3R0N/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-03-08 Released: 2011-04-27 
• Deposition Author(s): Ramagopal, U.A., Samanta, D., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

---

Experimental Data Snapshot

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

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

• PubMed: 22927415 
• 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 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
Molecule	Chains	Sequence Length	Organism	Details
Poliovirus receptor-related protein 2	A	128	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 57.964	α = 90.00
b = 57.964	β = 90.00
c = 67.544	γ = 90.00

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-08 
• Released Date: 2011-04-27 
• Deposition Author(s): Ramagopal, U.A., Samanta, D., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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