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Open data
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Basic information
Entry | Database: PDB / ID: 1ff5 | ||||||
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Title | STRUCTURE OF E-CADHERIN DOUBLE DOMAIN | ||||||
![]() | EPITHELIAL CADHERIN | ||||||
![]() | CELL ADHESION / E-cadherin / Ca-binding | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pertz, O. / Bozic, D. / Koch, A.W. / Fauser, C. / Brancaccio, A. / Engel, J. | ||||||
![]() | ![]() Title: A new crystal structure, Ca2+ dependence and mutational analysis reveal molecular details of E-cadherin homoassociation. Authors: Pertz, O. / Bozic, D. / Koch, A.W. / Fauser, C. / Brancaccio, A. / Engel, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.4 KB | Display | ![]() |
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PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.3 KB | Display | ![]() |
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Full document | ![]() | 388.4 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23919.590 Da / Num. of mol.: 2 / Fragment: DOUBLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.92 Å3/Da | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 50 mM ammonium sulfate, 50 mM NaOAc, 30% PEG 8000, pH 8.5, Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.93→20 Å / Num. all: 28520 / Num. obs: 28520 / % possible obs: 95.5 % / Rmerge(I) obs: 0.133 |
Reflection | *PLUS Num. obs: 13451 / Num. measured all: 28520 |
Reflection shell | *PLUS Highest resolution: 2.93 Å / Lowest resolution: 3 Å / % possible obs: 81.5 % |
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Processing
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Refinement | Resolution: 2.93→20 Å / Rfactor all: 0.1986 / σ(F): 0 / Stereochemistry target values: Engh & Huber | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.93→20 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.01 |