Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.41 kDa 
• Atom Count: 2512 
• Residue Count: 288 
• Unique protein chains: 1

1QZ1

Crystal Structure of the Ig 1-2-3 fragment of NCAM

• DOI: 10.2210/pdb1QZ1/pdb

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


• Deposited: 2003-09-15 Released: 2003-11-04 
• Deposition Author(s): Soroka, V., Kolkova, K., Kastrup, J.S., Diederichs, K., Breed, J., Kiselyov, V.V., Poulsen, F.M., Larsen, I.K., Welte, W., Berezin, V., Bock, E., Kasper, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.218 

Literature

Structure and interactions of NCAM Ig1-2-3 suggest a novel zipper mechanism for homophilic adhesion

Soroka, V., Kolkova, K., Kastrup, J.S., Diederichs, K., Breed, J., Kiselyov, V.V., Poulsen, F.M., Larsen, I.K., Welte, W., Berezin, V., Bock, E., Kasper, C.

(2003) Structure 11: 1291-1301

• PubMed: 14527396 
• DOI: 10.1016/j.str.2003.09.006
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The neural cell adhesion molecule, NCAM, mediates Ca(2+)-independent cell-cell and cell-substratum adhesion via homophilic (NCAM-NCAM) and heterophilic (NCAM-non-NCAM molecules) binding. NCAM plays a key role in neural development, regeneration, and synaptic plasticity, including learning and memory consolidation. The crystal structure of a fragment comprising the three N-terminal Ig modules of rat NCAM has been determined to 2.0 A resolution. Based on crystallographic data and biological experiments we present a novel model for NCAM homophilic binding. The Ig1 and Ig2 modules mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), whereas the Ig3 module mediates interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions) through simultaneous binding to the Ig1 and Ig2 modules. This arrangement results in two perpendicular zippers forming a double zipper-like NCAM adhesion complex.

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Related Citations: 

• 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

• Expression, crystallization and preliminary X-ray analysis of the two amino-terminal Ig domains of the neural cell adhesion molecule (NCAM)
  Kasper, C., Rasmussen, H., Berezin, V., Bock, E., Larsen, I.K.
  (1999) Acta Crystallogr D Biol Crystallogr 55: 1598

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Organizational Affiliation: 

Protein Laboratory, Institute of Molecular Pathology, Panum Institute, Blegdamsvej 3 C, DK-2200 Copenhagen, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Neural cell adhesion molecule 1, 140 kDa isoform	A	291	Rattus norvegicus	Mutation(s): 0  Gene Names: Ncam1, Ncam
Find proteins for P13596 (Rattus norvegicus) Explore P13596  Go to UniProtKB:  P13596

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.218 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.44	α = 90
b = 107.76	β = 90
c = 149.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-15 
• Released Date: 2003-11-04 
Deposition Author(s): Soroka, V., Kolkova, K., Kastrup, J.S., Diederichs, K., Breed, J., Kiselyov, V.V., Poulsen, F.M., Larsen, I.K., Welte, W., Berezin, V., Bock, E., Kasper, C.

Revision History 

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection