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Yorodumi- PDB-1gc6: CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN COMPLEXED WITH INOSI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gc6 | ||||||
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Title | CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN COMPLEXED WITH INOSITOL-(1,4,5)-TRIPHOSPHATE | ||||||
Components | RADIXIN | ||||||
Keywords | CELL ADHESION / CYTOSKELETON | ||||||
Function / homology | Function and homology information stereocilium base / regulation of organelle assembly / establishment of protein localization to plasma membrane / microvillus assembly / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / Recycling pathway of L1 / cell tip / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome ...stereocilium base / regulation of organelle assembly / establishment of protein localization to plasma membrane / microvillus assembly / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / Recycling pathway of L1 / cell tip / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / stereocilium / apical protein localization / barbed-end actin filament capping / cellular response to thyroid hormone stimulus / protein kinase A binding / positive regulation of G1/S transition of mitotic cell cycle / cortical actin cytoskeleton / microvillus / cleavage furrow / ruffle / cell adhesion molecule binding / T-tubule / protein kinase A signaling / filopodium / adherens junction / establishment of protein localization / apical part of cell / lamellipodium / myelin sheath / actin binding / regulation of cell shape / midbody / protein domain specific binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Tsukita, S. / Hakoshima, T. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain. Authors: Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Hakoshima, T. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallographic characterization of the membrane-binding domain of radixin Authors: Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Tsukita, S. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gc6.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gc6.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gc6_validation.pdf.gz | 872.6 KB | Display | wwPDB validaton report |
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Full document | 1gc6_full_validation.pdf.gz | 879.4 KB | Display | |
Data in XML | 1gc6_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1gc6_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gc6 ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gc6 | HTTPS FTP |
-Related 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: 35278.723 Da / Num. of mol.: 1 / Fragment: FERM DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P26043 |
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#2: Chemical | ChemComp-I3P / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.41 Å3/Da / Density % sol: 72.08 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES, INOSITOL-(1,4,5)-TRIPHOSPHATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 88728 / Num. obs: 14511 / % possible obs: 99.5 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.485 / % possible all: 98.8 |
Reflection shell | *PLUS % possible obs: 98.8 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.9→30 Å / σ(F): 2 / Stereochemistry target values: protein.para
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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