3R0N | pdb_00003r0n

Crystal Structure of the Immunoglobulin variable domain of Nectin-2

• PDB DOI: https://doi.org/10.2210/pdb3R0N/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.173 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

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

• PubMed: 22927415 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 14.01 kDa 
• Atom Count: 1,240 
• Modeled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor-related protein 2	A	128	Homo sapiens	Mutation(s): 0  Gene Names: HVEB, PRR2, PVRL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92692 (Homo sapiens) Explore Q92692  Go to UniProtKB:  Q92692
PHAROS:  Q92692 GTEx:  ENSG00000130202

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.173 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.964	α = 90
b = 57.964	β = 90
c = 67.544	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 1.6: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary