1QZ1 | pdb_00001qz1

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


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1QZ1

This is version 1.5 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/j.str.2003.09.006
  • Primary Citation Related Structures: 
    1QZ1

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 32.41 kDa 
  • Atom Count: 2,512 
  • Modeled Residue Count: 288 
  • Deposited Residue Count: 291 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neural cell adhesion molecule 1, 140 kDa isoform291Rattus norvegicusMutation(s): 0 
Gene Names: NCAM1
UniProt
Find proteins for P13596 (Rattus norvegicus)
Explore P13596 
Go to UniProtKB:  P13596
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13596
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.238 (Depositor) 
  • R-Value Work:  0.218 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.44α = 90
b = 107.76β = 90
c = 149.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary