1EPF

CRYSTAL STRUCTURE OF THE TWO N-TERMINAL IMMUNOGLOBULIN DOMAINS OF THE NEURAL CELL ADHESION MOLECULE (NCAM)

• PDB DOI: https://doi.org/10.2210/pdb1EPF/pdb

• Classification: CELL ADHESION
• Organism(s): Rattus norvegicus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2000-03-29 Released: 2000-10-09 
• Deposition Author(s): Kasper, C., Rasmussen, H., Kastrup, J.S., Ikemizu, S., Jones, E.Y., Berezin, V., Bock, E., Larsen, I.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.234 (Depositor) 
• R-Value Work: 
  0.201 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Structural basis of cell-cell adhesion by NCAM.

Kasper, C., Rasmussen, H., Kastrup, J.S., Ikemizu, S., Jones, E.Y., Berezin, V., Bock, E., Larsen, I.K.

(2000) Nat Struct Biol 7: 389-393

• PubMed: 10802736 
• DOI: https://doi.org/10.1038/75165
• Primary Citation of Related Structures:  
  1EPF


• PubMed Abstract: 
  

  The neural cell adhesion molecule NCAM, a member of the immunoglobulin superfamily, mediates cell-cell recognition and adhesion via a homophilic interaction. NCAM plays a key role during development and regeneration of the nervous system and is involved in synaptic plasticity associated with memory and learning. The 1.85 A crystal structure of the two N-terminal extracellular domains of NCAM reported here provides a structural basis for the homophilic interaction. The molecular packing of the two-domain structure reveals a cross shaped antiparallel dimer, and provides fundamental insight into trans-cellular recognition mediated by NCAM.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen O, Denmark.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.67 kDa 
• Atom Count: 7,622 
• Modelled Residue Count: 761 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (NEURAL CELL ADHESION MOLECULE)	A, B, C, D	191	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P13596 (Rattus norvegicus) Explore P13596  Go to UniProtKB:  P13596

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.234 (Depositor) 
• R-Value Work:  0.201 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.078	α = 90
b = 122.505	β = 98.27
c = 72.859	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-10-09 
Deposition Author(s): Kasper, C., Rasmussen, H., Kastrup, J.S., Ikemizu, S., Jones, E.Y., Berezin, V., Bock, E., Larsen, I.K.

Revision History  

• Version 1.0: 2000-10-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary