Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 44713.06 
• Atom Count: 3093 
• Residue Count: 389 
• Unique protein chains: 1

2JLL

Crystal structure of NCAM2 IgIV-FN3II

• DOI: 10.2210/pdb2JLL/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris


• Deposited: 2008-09-10 Released: 2009-11-17 
• Deposition Author(s): Kulahin, N., Rasmussen, K., Kristensen, O., Kastrup, J., Berezin, V., Bock, E., Walmod, P., Gajhede, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 

Literature

Structural Model and Trans-Interaction of the Entire Ectodomain of the Olfactory Cell Adhesion Molecule.

Kulahin, N., Kristensen, O., Rasmussen, K.K., Olsen, L., Rydberg, P., Vestergaard, B., Kastrup, J.S., Berezin, V., Bock, E., Walmod, P.S., Gajhede, M.

(2011) Structure 19: 203

• PubMed: 21300289 
• DOI: 10.1016/j.str.2010.12.014
• Primary Citation of Related Structures:  
  2WIM, 2XYC, 2XY2, 2XY1, 2V5T


• PubMed Abstract: 
  

The ectodomain of olfactory cell adhesion molecule (OCAM/NCAM2/RNCAM) consists of five immunoglobulin (Ig) domains (IgI-V), followed by two fibronectin-type 3 (Fn3) domains (Fn3I-II). A complete structural model of the entire ectodomain of human OCAM has been assembled from crystal structures of six recombinant proteins corresponding to different regions of the ectodomain. The model is the longest experimentally based composite structural model of an entire IgCAM ectodomain. It displays an essentially linear arrangement of IgI-V, followed by bends between IgV and Fn3I and between Fn3I and Fn3II. Proteins containing IgI-IgII domains formed stable homodimers in solution and in crystals. Dimerization could be disrupted in vitro by mutations in the dimer interface region. In conjunction with the bent ectodomain conformation, which can position IgI-V parallel with the cell surface, the IgI-IgII dimerization enables OCAM-mediated trans-interactions with an intercellular distance of about 20 nm, which is consistent with that observed in synapses.

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Organizational Affiliation: 

Protein Laboratory, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NEURAL CELL ADHESION MOLECULE 2	A	389	Homo sapiens	Mutation(s): 0  Gene Names: NCAM2 (NCAM21)
Find proteins for O15394 (Homo sapiens) Go to Gene View: NCAM2 Go to UniProtKB:  O15394

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 151.740	α = 90.00
b = 33.800	β = 98.36
c = 97.670	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
MOSFLM	data reduction
PHENIX	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-10 
• Released Date: 2009-11-17 
• Deposition Author(s): Kulahin, N., Rasmussen, K., Kristensen, O., Kastrup, J., Berezin, V., Bock, E., Walmod, P., Gajhede, M.

Revision History 

• Version 1.0: 2009-11-17
  Type: Initial release
• Version 1.1: 2011-05-07
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance