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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.51 kDa 
• Atom Count: 3337 
• Residue Count: 390 
• Unique protein chains: 1

3P40

Crystal structure of neurofascin adhesion complex in space group p3221

• DOI: 10.2210/pdb3P40/pdb

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


• Deposited: 2010-10-05 Released: 2010-11-03 
• Deposition Author(s): Liu, H., He, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.316 
• R-Value Work: 0.273 
• R-Value Observed: 0.273 

Literature

Homophilic adhesion mechanism of neurofascin, a member of the l1 family of neural cell adhesion molecules.

Liu, H., Focia, P.J., He, X.

(2011) J Biol Chem 286: 797-805

• PubMed: 21047790 
• DOI: 10.1074/jbc.M110.180281
• Primary Citation of Related Structures:  
  3P40, 3P3Y


• PubMed Abstract: 
  

The L1 family neural cell adhesion molecules play key roles in specifying the formation and remodeling of the neural network, but their homophilic interaction that mediates adhesion is not well understood. We report two crystal structures of a dimeric form of the headpiece of neurofascin, an L1 family member. The four N-terminal Ig-like domains of neurofascin form a horseshoe shape, akin to several other immunoglobulin superfamily cell adhesion molecules such as hemolin, axonin, and Dscam. The neurofascin dimer, captured in two crystal forms with independent packing patterns, reveals a pair of horseshoes in trans-synaptic adhesion mode. The adhesion interaction is mediated mostly by the second Ig-like domain, which features an intermolecular β-sheet formed by the joining of two individual GFC β-sheets and a large but loosely packed hydrophobic cluster. Mutagenesis combined with gel filtration assays suggested that the side chain hydrogen bonds at the intermolecular β-sheet are essential for the homophilic interaction and that the residues at the hydrophobic cluster play supplementary roles. Our structures reveal a conserved homophilic adhesion mode for the L1 family and also shed light on how the pathological mutations of L1 affect its structure and function.

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Organizational Affiliation: 

Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurofascin	A	404	Homo sapiens	Mutation(s): 0  Gene Names: NFASC, KIAA0756
Find proteins for O94856 (Homo sapiens) Explore O94856  Go to UniProtKB:  O94856
NIH Common Fund Data Resources
PHAROS:  O94856 GTEx:  ENSG00000163531

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: 3.20 Å
• R-Value Free: 0.316 
• R-Value Work: 0.273 
• R-Value Observed: 0.273 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.508	α = 90
b = 94.508	β = 90
c = 126.723	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-05 
• Released Date: 2010-11-03 
Deposition Author(s): Liu, H., He, X.

Revision History 

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary