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Yorodumi- PDB-7ds3: Crystal structure of actin capping protein in complex with twinfl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ds3 | ||||||||||||
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Title | Crystal structure of actin capping protein in complex with twinflin-2 C-terminus tail | ||||||||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / actin dynamics / actin capping protein / twinfilin / CARMIL / V-1 | ||||||||||||
Function / homology | Function and homology information 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 / regulation of microvillus length / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / WASH complex / sperm connecting piece ...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 / regulation of microvillus length / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / WASH complex / sperm connecting piece / F-actin capping protein complex / negative regulation of filopodium assembly / sequestering of actin monomers / negative regulation of actin filament polymerization / stereocilium / cell projection organization / cell junction assembly / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / cortical cytoskeleton / myofibril / brush border / actin monomer binding / positive regulation of axon extension / positive regulation of lamellipodium assembly / cytoskeleton organization / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / filopodium / actin filament / protein kinase C binding / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / cell morphogenesis / positive regulation of neuron projection development / Z disc / cellular response to growth factor stimulus / actin filament binding / lamellipodium / growth cone / actin cytoskeleton organization / postsynaptic density / intracellular signal transduction / perinuclear region of cytoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å | ||||||||||||
Authors | Takeda, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ds3.cif.gz | 257.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ds3.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ds3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/7ds3 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7ds3 | HTTPS FTP |
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-Related structure data
Related structure data | 7ds2SC 7ds4C 7ds6C 7ds8C 7dsaC 7dsbC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 33001.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13127 |
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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.) Gallus gallus (chicken) / Gene: CAPZB / Production host: Escherichia coli (E. coli) / References: UniProt: P14315 |
#3: Protein/peptide | Mass: 3293.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9Z0P5 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% (w/v) PEG 3350, 50mM Tris-HCl (pH = 7.0) |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 16, 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: 2.09→49.17 Å / Num. obs: 34883 / % possible obs: 99.9 % / Redundancy: 7.148 % / Biso Wilson estimate: 46.149 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.062 / Χ2: 0.87 / Net I/σ(I): 22.82 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ds2 Resolution: 2.09→49.17 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.9326 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: 48.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→49.17 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.57499558445 Å / Origin y: -17.2812431369 Å / Origin z: -19.7459615774 Å
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Refinement TLS group | Selection details: all |