+Open data
-Basic information
Entry | Database: PDB / ID: 1ncj | ||||||
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Title | N-CADHERIN, TWO-DOMAIN FRAGMENT | ||||||
Components | PROTEIN (N-CADHERIN) | ||||||
Keywords | CELL ADHESION PROTEIN | ||||||
Function / homology | Function and homology information mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / regulation of postsynaptic density protein 95 clustering / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / desmosome ...mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / regulation of postsynaptic density protein 95 clustering / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / desmosome / synaptic vesicle clustering / gamma-catenin binding / neural crest cell development / glial cell differentiation / telencephalon development / neuroepithelial cell differentiation / type B pancreatic cell development / cell-cell adhesion mediated by cadherin / neuronal stem cell population maintenance / alpha-catenin binding / fascia adherens / apicolateral plasma membrane / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Myogenesis / regulation of Rho protein signal transduction / postsynaptic specialization membrane / brain morphogenesis / catenin complex / cell-cell junction assembly / adherens junction organization / blood vessel morphogenesis / regulation of myelination / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cortical actin cytoskeleton / regulation of axonogenesis / nitric-oxide synthase binding / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane raft / intercalated disc / homeostasis of number of cells / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / T-tubule / synapse assembly / striated muscle cell differentiation / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / brain development / modulation of chemical synaptic transmission / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / sarcolemma / cerebral cortex development / beta-catenin binding / cell-cell adhesion / regulation of protein localization / cell-cell junction / cell migration / apical part of cell / lamellipodium / basolateral plasma membrane / protein phosphatase binding / positive regulation of MAPK cascade / postsynaptic density / cell adhesion / neuron projection / cadherin binding / apical plasma membrane / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein kinase binding / enzyme binding / cell surface / protein-containing complex / RNA binding / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Tamura, K. / Shan, W.-S. / Hendrickson, W.A. / Colman, D.R. / Shapiro, L. | ||||||
Citation | Journal: Neuron / Year: 1998 Title: Structure-function analysis of cell adhesion by neural (N-) cadherin. Authors: Tamura, K. / Shan, W.S. / Hendrickson, W.A. / Colman, D.R. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ncj.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ncj.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ncj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1ncj ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1ncj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23603.465 Da / Num. of mol.: 1 / Fragment: TWO-DOMAIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Tissue: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P15116 | ||
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#2: Chemical | #3: Chemical | ChemComp-IUM / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.15 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: REMARK 280 CRYSTALLIZATION CONDITIONS: REMARK 280 HANGING DROP, 20MG/ML PROTEIN REMARK 280 50 MM NA ACETATE, PH 5.0, 15MM CACL2, REMARK 280 1MM UO2 ACETATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: drop contains equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→20 Å / Num. obs: 9451 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.93 / Rsym value: 0.93 / Net I/σ(I): 12.96 |
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.12 / Rsym value: 0.322 / % possible all: 97.7 |
Reflection shell | *PLUS % possible obs: 97.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NCG AND 1EDH Resolution: 3.4→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 29.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.55 Å / Total num. of bins used: 8 / % reflection obs: 97 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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