+Open data
-Basic information
Entry | Database: PDB / ID: 3lng | ||||||
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Title | Crystal structure of E-cadherin EC12 AA extension | ||||||
Components | Cadherin-1 | ||||||
Keywords | CELL ADHESION / cadherin / Calcium / Cell junction / Cell membrane / Cleavage on pair of basic residues / Glycoprotein / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / Adherens junctions interactions / Degradation of the extracellular matrix / positive regulation of cell-cell adhesion / Integrin cell surface interactions ...uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / Adherens junctions interactions / Degradation of the extracellular matrix / positive regulation of cell-cell adhesion / Integrin cell surface interactions / lateral loop / regulation of neuron migration / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / regulation of protein localization to cell surface / trophectodermal cell differentiation / alpha-catenin binding / epithelial cell morphogenesis / Schmidt-Lanterman incisure / bicellular tight junction assembly / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / intestinal epithelial cell development / node of Ranvier / protein metabolic process / catenin complex / cell-cell junction assembly / negative regulation of protein processing / adherens junction organization / negative regulation of protein localization to plasma membrane / apical junction complex / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / decidualization / canonical Wnt signaling pathway / establishment of skin barrier / axon terminus / synapse assembly / cytoskeletal protein binding / embryo implantation / protein tyrosine kinase binding / protein localization to plasma membrane / cell periphery / adherens junction / sensory perception of sound / cellular response to amino acid stimulus / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cell-cell adhesion / beta-catenin binding / negative regulation of epithelial cell proliferation / regulation of protein localization / cell-cell junction / cell migration / apical part of cell / actin cytoskeleton organization / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding / in utero embryonic development / postsynapse / molecular adaptor activity / endosome / cadherin binding / protein domain specific binding / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / cell surface / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Harrison, O. / Jin, X. / Shapiro, L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Two-step adhesive binding by classical cadherins. Authors: Harrison, O.J. / Bahna, F. / Katsamba, P.S. / Jin, X. / Brasch, J. / Vendome, J. / Ahlsen, G. / Carroll, K.J. / Price, S.R. / Honig, B. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lng.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lng.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 3lng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/3lng ftp://data.pdbj.org/pub/pdb/validation_reports/ln/3lng | HTTPS FTP |
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-Related structure data
Related structure data | 3lndC 3lneC 3lnfC 3lnhC 3lniC 1edhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23403.021 Da / Num. of mol.: 2 / Fragment: UNP residues 157-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09803 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.88 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 0.1M Tris, pH 8.5, 1.3M ammonium sulfate, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2007 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 13698 / % possible obs: 81.4 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDH Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.68→2.75 Å / Total num. of bins used: 20
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