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- PDB-1o6s: Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o6s | ||||||
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Title | Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex | ||||||
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![]() | BACTERIAL INFECTION / LEUCINE RICH REPEAT / CELL ADHESION / CELL-WALL SURFACE PROTEIN | ||||||
Function / homology | ![]() response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Formation of definitive endoderm ...response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Formation of definitive endoderm / Adherens junctions interactions / catenin complex / Apoptotic cleavage of cell adhesion proteins / GTPase activating protein binding / cell-cell junction assembly / adherens junction organization / apical junction complex / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / RHO GTPases activate IQGAPs / Integrin cell surface interactions / cell adhesion molecule binding / synapse assembly / InlA-mediated entry of Listeria monocytogenes into host cells / Degradation of the extracellular matrix / negative regulation of cell migration / peptidoglycan-based cell wall / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / cell morphogenesis / trans-Golgi network / cytoplasmic side of plasma membrane / response to toxic substance / beta-catenin binding / cell-cell adhesion / positive regulation of protein import into nucleus / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / actin cytoskeleton / lamellipodium / cell junction / postsynapse / regulation of gene expression / endosome / response to xenobiotic stimulus / cadherin binding / glutamatergic synapse / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schubert, W.-D. / Urbanke, C. / Ziehm, T. / Beier, V. / Machner, M.P. / Domann, E. / Wehland, J. / Chakraborty, T. / Heinz, D.W. | ||||||
![]() | ![]() Title: Structure of Internalin, a Major Invasion Protein of Listeria Monocytogenes, in Complex with its Human Receptor E-Cadherin Authors: Schubert, W.-D. / Urbanke, C. / Ziehm, T. / Beier, V. / Machner, M.P. / Domann, E. / Wehland, J. / Chakraborty, T. / Heinz, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.2 KB | Display | ![]() |
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PDB format | ![]() | 108.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.7 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 50239.133 Da / Num. of mol.: 1 / Fragment: FUNCTIONAL DOMAIN, RESIDUES 36-496 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 11523.009 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 156-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | FIRST FIVE RESIDUES (GPLGS) INTRODUCED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: VAPOUR DIFFUSION / HANGING DROP 10 MG/ML IN 10 MM HEPES PH 7.0, 26% PEG 4000, 100 MM MES/TRIS PH 7.0, 100 MM SODIUM ACETATE, 50 MM CACL2 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.1 Å / Num. obs: 50336 / % possible obs: 92 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.4 / % possible all: 84.3 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 25 Å / Num. obs: 46306 |
Reflection shell | *PLUS % possible obs: 84.3 % |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→69.01 Å
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Refine LS restraints |
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