+Open data
-Basic information
Entry | Database: PDB / ID: 1ncg | ||||||
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Title | STRUCTURAL BASIS OF CELL-CELL ADHESION BY CADHERINS | ||||||
Components | N-CADHERINCadherin-2 | ||||||
Keywords | CELL ADHESION PROTEIN / CADHERIN | ||||||
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 / neural crest cell development / gamma-catenin binding / glial cell differentiation / cell-cell adhesion mediated by cadherin / telencephalon development / neuroepithelial cell differentiation / type B pancreatic cell development / 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 / regulation of axonogenesis / cortical actin cytoskeleton / nitric-oxide synthase binding / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane raft / homeostasis of number of cells / intercalated disc / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / synapse assembly / striated muscle cell differentiation / T-tubule / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / brain development / negative regulation of canonical Wnt signaling pathway / sarcolemma / modulation of chemical synaptic transmission / cell morphogenesis / cell-cell adhesion / cerebral cortex development / beta-catenin binding / regulation of protein localization / cell-cell junction / cell migration / apical part of cell / lamellipodium / cell junction / basolateral plasma membrane / protein phosphatase binding / postsynaptic density / positive regulation of MAPK cascade / 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 / Resolution: 2.1 Å | ||||||
Authors | Shapiro, L. / Fannon, A.M. / Kwong, P.D. / Thompson, A. / Lehmann, M.S. / Grubel, G. / Legrand, J.-F. / Als-Nielsen, J. / Colman, D.R. / Hendrickson, W.A. | ||||||
Citation | Journal: Nature / Year: 1995 Title: Structural basis of cell-cell adhesion by cadherins. Authors: Shapiro, L. / Fannon, A.M. / Kwong, P.D. / Thompson, A. / Lehmann, M.S. / Grubel, G. / Legrand, J.F. / Als-Nielsen, J. / Colman, D.R. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ncg.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ncg.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ncg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1ncg ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1ncg | 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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Atom site foot note | 1: CIS PROLINE - PRO 16 / 2: CIS PROLINE - PRO 18 / 3: CIS PROLINE - PRO 47 | ||||||||
Details | THE ASYMMETRIC UNIT CONTAINS A SINGLE MOLECULE. A CADHERIN STRAND DIMER IS FORMED WITH THE (Y, X, -Z) SYMMETRY MATE. AN ADHESION DIMER IS FORMED WITH THE (1-Y, 1-X, 1/2-Z) SYMMETRY MATE. NOTE THAT THESE TRANSFORMATIONS ARE IN THE NON-ORTHOGONAL HEXAGONAL LATTICE. |
-Components
#1: Protein | Mass: 12244.817 Da / Num. of mol.: 1 Mutation: PCR MUTATION D27G, CLONING ARTIFACT GIVES TWO EXTRA RESIDUES (GLY-SER) AT N-TERMINUS (INS(G-2,S-1)) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P15116 |
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#2: Chemical | ChemComp-YB / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE MODEL INCLUDES ONE YTTERBIUM ION (YB 3+) BOUND AT THE PUTATIVE CALCIUM BINDING SITE. |
Sequence details | RESIDUE NUMBERING IS FOR THE MATURE PROTEIN. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A |
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Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1994 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 18803 / % possible obs: 93.4 % / Rmerge(I) obs: 0.045 |
Reflection | *PLUS Rmerge(I) obs: 0.045 |
-Processing
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Refinement | Resolution: 2.1→5 Å / σ(F): 2
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Displacement parameters | Biso mean: 26.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→5 Å
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Refine LS restraints |
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