1NCJ | pdb_00001ncj

N-CADHERIN, TWO-DOMAIN FRAGMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.321 (Depositor) 
  • R-Value Work: 
    0.212 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure-function analysis of cell adhesion by neural (N-) cadherin.

Tamura, K.Shan, W.S.Hendrickson, W.A.Colman, D.R.Shapiro, L.

(1998) Neuron 20: 1153-1163

  • DOI: https://doi.org/10.1016/s0896-6273(00)80496-1
  • Primary Citation Related Structures: 
    1NCJ

  • PubMed Abstract: 

    To investigate the possible biological function of the lateral "strand dimer" observed in crystal structures of a D1 domain extracellular fragment from N-cadherin, we have undertaken site-directed mutagenesis studies of this molecule. Mutation of most residues important in the strand dimer interface abolish the ability of N-cadherin to mediate cell adhesion. Mutation of an analogous central residue (Trp-2) in E-cadherin also abrogates the adhesive capacity of that molecule. We also determined the crystal structure of a Ca2+-complexed two-domain fragment from N-cadherin. This structure, like its E-cadherin counterpart, does not adopt the strand dimer conformation. This suggests the possibility that classical cadherins might stably exist in both dimeric and monomeric forms. Data from several laboratories imply that lateral dimerization or clustering of cadherins may increase their adhesivity. We suggest the possibility that the strand dimer may play a role in this activation.


  • Organizational Affiliation
    • Brookdale Center for Developmental and Molecular Biology, Mount Sinai School of Medicine, New York, New York 10029, USA.

Macromolecule Content 

  • Total Structure Weight: 23.99 kDa 
  • Atom Count: 1,542 
  • Modeled Residue Count: 214 
  • Deposited Residue Count: 215 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (N-CADHERIN)215Mus musculusMutation(s): 0 
UniProt
Find proteins for P15116 (Mus musculus)
Explore P15116 
Go to UniProtKB:  P15116
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15116
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.321 (Depositor) 
  • R-Value Work:  0.212 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99α = 90
b = 99β = 90
c = 136.1γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description