+Open data
-Basic information
Entry | Database: PDB / ID: 3q2l | ||||||
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Title | Mouse E-cadherin EC1-2 V81D mutant | ||||||
Components | Cadherin-1 | ||||||
Keywords | CELL ADHESION / beta barrel fold / extracellular cadherin (EC) domain / Cell-cell adhesion molecule / Membrane | ||||||
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.J. / Jin, X. / Shapiro, L. | ||||||
Citation | Journal: Structure / Year: 2011 Title: The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Authors: Harrison, O.J. / Jin, X. / Hong, S. / Bahna, F. / Ahlsen, G. / Brasch, J. / Wu, Y. / Vendome, J. / Felsovalyi, K. / Hampton, C.M. / Troyanovsky, R.B. / Ben-Shaul, A. / Frank, J. / ...Authors: Harrison, O.J. / Jin, X. / Hong, S. / Bahna, F. / Ahlsen, G. / Brasch, J. / Wu, Y. / Vendome, J. / Felsovalyi, K. / Hampton, C.M. / Troyanovsky, R.B. / Ben-Shaul, A. / Frank, J. / Troyanovsky, S.M. / Shapiro, L. / Honig, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q2l.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q2l.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 3q2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/3q2l ftp://data.pdbj.org/pub/pdb/validation_reports/q2/3q2l | HTTPS FTP |
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-Related structure data
Related structure data | 3q2nC 3q2vC 3q2wC 2qvfS 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: 23276.822 Da / Num. of mol.: 2 / Fragment: E-cadherin EC1-2 fragment, residues 157-369 / Mutation: V81D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh1 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09803 #2: Chemical | ChemComp-CA / #3: Chemical | #4: 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: 8.49 Å3/Da / Density % sol: 85.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10% (v/v) PEG 400, 0.1M sodium acetate pH4.6, 0.13M CaCl2, Cryoprotected by increasing PEG 400 to 30%, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 43603 / Num. obs: 43500 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.135 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 4289 / Rsym value: 0.539 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QVF Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / ESU R Free: 0.2 / 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: 43.496 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.759 Å / Total num. of bins used: 20
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