+Open data
-Basic information
Entry | Database: PDB / ID: 3lne | ||||||
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Title | Crystal structure of E-cadherin EC12 K14E | ||||||
Components | Cadherin-1 | ||||||
Keywords | CELL ADHESION / cadherin / Calcium / Cell junction / Cell membrane / Glycoprotein / 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 / flotillin complex / Schmidt-Lanterman incisure / bicellular tight junction assembly / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / intestinal epithelial cell development / node of Ranvier / protein metabolic process / catenin complex / negative regulation of protein processing / cell-cell junction assembly / negative regulation of protein localization to plasma membrane / adherens junction organization / 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 / cell periphery / protein localization to plasma membrane / adherens junction / sensory perception of sound / cellular response to amino acid stimulus / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / beta-catenin binding / cell-cell adhesion / negative regulation of epithelial cell proliferation / regulation of protein localization / cell-cell junction / apical part of cell / actin cytoskeleton organization / postsynapse / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding / in utero embryonic development / 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 Å | ||||||
Authors | Jin, X. / Harrison, O. / 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 | 3lne.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lne.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 3lne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lne_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 3lne_full_validation.pdf.gz | 428.3 KB | Display | |
Data in XML | 3lne_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3lne_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/3lne ftp://data.pdbj.org/pub/pdb/validation_reports/ln/3lne | HTTPS FTP |
-Related structure data
Related structure data | 3lndC 3lnfC 3lngC 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: 23260.801 Da / Num. of mol.: 1 / Fragment: UNP residues 157-369 / Mutation: K14E 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 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH 6.5, 0.75M sodium sulfate, 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: 0.97897 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97897 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 21629 / Num. obs: 19964 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDH Resolution: 2→20 Å / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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