Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.73 kDa 
• Atom Count: 2588 
• Residue Count: 302 
• Unique protein chains: 1

4FOM

Crystal structure of human nectin-3 full ectodomain (D1-D3)

• DOI: 10.2210/pdb4FOM/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-06-20 Released: 2012-08-22 
• Deposition Author(s): Harrison, O.J., Jin, X., Brasch, J., Shapiro, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.93 Å
• R-Value Free: 0.279 
• R-Value Work: 0.247 
• R-Value Observed: 0.248 

Literature

Nectin ectodomain structures reveal a canonical adhesive interface.

Harrison, O.J., Vendome, J., Brasch, J., Jin, X., Hong, S., Katsamba, P.S., Ahlsen, G., Troyanovsky, R.B., Troyanovsky, S.M., Honig, B., Shapiro, L.

(2012) Nat Struct Mol Biol 19: 906-915

• PubMed: 22902367 
• DOI: 10.1038/nsmb.2366
• Primary Citation of Related Structures:  
  4FOM, 4FQP, 4FRW, 4FS0, 4FMK, 4FN0, 4FMF


• PubMed Abstract: 
  

Nectins are immunoglobulin superfamily glycoproteins that mediate intercellular adhesion in many vertebrate tissues. Homophilic and heterophilic interactions between nectin family members help mediate tissue patterning. We determined the homophilic binding affinities and heterophilic specificities of all four nectins and the related protein nectin-like 5 (Necl-5) from human and mouse, revealing a range of homophilic interaction strengths and a defined heterophilic specificity pattern. To understand the molecular basis of their adhesion and specificity, we determined the crystal structures of natively glycosylated full ectodomains or adhesive fragments of all four nectins and Necl-5. All of the crystal structures revealed dimeric nectins bound through a stereotyped interface that was previously proposed to represent a cis dimer. However, conservation of this interface and the results of targeted cross-linking experiments showed that this dimer probably represents the adhesive trans interaction. The structure of the dimer provides a simple molecular explanation for the adhesive binding specificity of nectins.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor-related protein 3	A	308	Homo sapiens	Mutation(s): 0  Gene Names: PVRL3, PRR3, NECTIN3
Find proteins for Q9NQS3 (Homo sapiens) Explore Q9NQS3  Go to UniProtKB:  Q9NQS3
NIH Common Fund Data Resources
PHAROS:  Q9NQS3 GTEx:  ENSG00000177707

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, E	5		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	6		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.93 Å
• R-Value Free: 0.279 
• R-Value Work: 0.247 
• R-Value Observed: 0.248 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.867	α = 90
b = 131.867	β = 90
c = 247.543	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-20 
• Released Date: 2012-08-22 
Deposition Author(s): Harrison, O.J., Jin, X., Brasch, J., Shapiro, L.

Revision History 

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2012-09-05
  Changes: Database references
• Version 1.2: 2012-09-26
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary