2JLL

Crystal structure of NCAM2 IgIV-FN3II

• PDB DOI:  https://doi.org/10.2210/pdb2JLL/pdb

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


• 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: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

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: https://doi.org/10.1016/j.str.2010.12.014
• Primary Citation of Related Structures:  
  2JLL, 2V5T, 2WIM, 2XY1, 2XY2, 2XYC


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 44.71 kDa 
• Atom Count: 3,240 
• Modelled Residue Count: 382 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEURAL CELL ADHESION MOLECULE 2	A	389	Homo sapiens	Mutation(s): 0  Gene Names: NCAM2, NCAM21
UniProt & NIH Common Fund Data Resources
Find proteins for O15394 (Homo sapiens) Explore O15394  Go to UniProtKB:  O15394
PHAROS:  O15394

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.74	α = 90
b = 33.8	β = 98.36
c = 97.67	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary