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Yorodumi- PDB-8hyi: Crystal structure of human P-cadherin MEC12 (X dimer) in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hyi | ||||||||||||||||||||||||
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Title | Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine | ||||||||||||||||||||||||
Components | Cadherin-3 | ||||||||||||||||||||||||
Keywords | CELL ADHESION / inhibitor | ||||||||||||||||||||||||
Function / homology | Function and homology information negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / retina homeostasis ...negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / retina homeostasis / Adherens junctions interactions / cell-cell junction assembly / adherens junction organization / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell adhesion via plasma membrane adhesion molecules / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / cell morphogenesis / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / cell migration / cell junction / cell adhesion / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å | ||||||||||||||||||||||||
Authors | Senoo, A. / Ito, S. / Ueno, G. / Nagatoishi, S. / Tsumoto, K. | ||||||||||||||||||||||||
Funding support | Japan, 7items
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Citation | Journal: Protein Sci. / Year: 2023 Title: Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion. Authors: Senoo, A. / Nagatoishi, S. / Kuroda, D. / Ito, S. / Ueno, G. / Caaveiro, J.M.M. / Tsumoto, K. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hyi.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hyi.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 8hyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hyi_validation.pdf.gz | 887.4 KB | Display | wwPDB validaton report |
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Full document | 8hyi_full_validation.pdf.gz | 900.8 KB | Display | |
Data in XML | 8hyi_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 8hyi_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/8hyi ftp://data.pdbj.org/pub/pdb/validation_reports/hy/8hyi | HTTPS FTP |
-Related structure data
Related structure data | 4zmqS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23422.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Production host: Escherichia coli (E. coli) / References: UniProt: P22223 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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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: 4.57 Å3/Da / Density % sol: 73.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.075M HEPES sodium pH 7.5, 1.125M Lithium sulfate monohydrate, 25% v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Oct 27, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→47.31 Å / Num. obs: 20527 / % possible obs: 99.9 % / Redundancy: 7.329 % / Biso Wilson estimate: 57.946 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.252 / Rrim(I) all: 0.271 / Χ2: 0.8 / Net I/σ(I): 9.7 / Num. measured all: 150449 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4zmq Resolution: 2.85→47.31 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.61 Å2 / Biso mean: 66.1267 Å2 / Biso min: 16.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→47.31 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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