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- PDB-7dsb: Crystal structure of actin capping protein in complex with V-1 an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dsb | ||||||||||||
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Title | Crystal structure of actin capping protein in complex with V-1 and twinfilin C-terminal tail | ||||||||||||
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![]() | CYTOSOLIC PROTEIN / actin dynamics / actin capping protein / twinfilin / CARMIL / V-1 | ||||||||||||
Function / homology | ![]() positive regulation of macromolecule biosynthetic process / regulation of barbed-end actin filament capping / regulation of actin phosphorylation / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / RHOBTB2 GTPase cycle / COPI-mediated anterograde transport ...positive regulation of macromolecule biosynthetic process / regulation of barbed-end actin filament capping / regulation of actin phosphorylation / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / RHOBTB2 GTPase cycle / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / cerebellar granule cell differentiation / regulation of striated muscle tissue development / BRCA1-BARD1 complex / WASH complex / : / F-actin capping protein complex / BRCA1-A complex / negative regulation of filopodium assembly / sequestering of actin monomers / skeletal muscle tissue regeneration / negative regulation of actin filament polymerization / catecholamine metabolic process / protein K6-linked ubiquitination / cell junction assembly / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / regulation of cell size / myofibril / cortical cytoskeleton / positive regulation of cardiac muscle hypertrophy / brush border / actin monomer binding / cytoskeleton organization / striated muscle cell differentiation / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of protein metabolic process / hippocampal mossy fiber to CA3 synapse / filopodium / actin filament / Schaffer collateral - CA1 synapse / cell morphogenesis / neuron differentiation / positive regulation of neuron projection development / Z disc / cellular response to mechanical stimulus / ubiquitin-protein transferase activity / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / regulation of translation / positive regulation of NF-kappaB transcription factor activity / actin cytoskeleton organization / positive regulation of cell growth / protein tyrosine kinase activity / sequence-specific DNA binding / postsynaptic density / axon / protein-containing complex binding / perinuclear region of cytoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Takeda, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail. Authors: Takeda, S. / Koike, R. / Fujiwara, I. / Narita, A. / Miyata, M. / Ota, M. / Maeda, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154 KB | Display | ![]() |
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PDB format | ![]() | 108.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451 KB | Display | ![]() |
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Full document | ![]() | 454.6 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ds2C ![]() 7ds3C ![]() 7ds4C ![]() 7ds6C ![]() 7ds8C ![]() 7dsaC ![]() 3aaaS S: Starting model for refinement C: citing same article ( |
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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: 33001.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 27473.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 13324.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein/peptide | Mass: 3331.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% (w/v) PEG 3350, 5% (v/v) isopropanol, 0.1M HEPES-NaOH (pH = 7.5) |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 12, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→45.84 Å / Num. obs: 28229 / % possible obs: 99.8 % / Redundancy: 6.009 % / Biso Wilson estimate: 50.147 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.107 / Χ2: 0.858 / Net I/σ(I): 15.84 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3aaa Resolution: 2.44→45.84 Å / SU ML: 0.3142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.407 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 51.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→45.84 Å
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Refine LS restraints |
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LS refinement shell |
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