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Yorodumi- PDB-7ds2: Crystal structure of actin capping protein in complex with twinfl... -
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-Basic information
Entry | Database: PDB / ID: 7ds2 | ||||||||||||
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Title | Crystal structure of actin capping protein in complex with twinflin-1 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 / RHOBTB2 GTPase cycle / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / WASH complex ...: / 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 / WASH complex / : / F-actin capping protein complex / negative regulation of filopodium assembly / sequestering of actin monomers / negative regulation of actin filament polymerization / cell junction assembly / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / myofibril / cortical cytoskeleton / positive regulation of cardiac muscle hypertrophy / brush border / actin monomer binding / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / filopodium / actin filament / cell morphogenesis / Schaffer collateral - CA1 synapse / Z disc / positive regulation of neuron projection development / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / protein tyrosine kinase activity / actin cytoskeleton organization / postsynaptic density / protein-containing complex binding / perinuclear region of cytoplasm / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 7ds2.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ds2.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ds2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ds2_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 7ds2_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 7ds2_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 7ds2_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/7ds2 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7ds2 | HTTPS FTP |
-Related structure data
Related structure data | 7ds3C 7ds4C 7ds6C 7ds8C 7dsaC 7dsbC 3aa7S 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: 4331.960 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Twf1, Ptk9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YR1 |
#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: 1.99 Å3/Da / Density % sol: 38.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 22.5% (w/v) PEG 400, 0.1M HEPES-NaOH (pH = 7.0) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 26, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→48.97 Å / Num. obs: 37412 / % possible obs: 96.5 % / Redundancy: 7.109 % / Biso Wilson estimate: 31.802 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.044 / Χ2: 0.971 / Net I/σ(I): 31.64 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3aa7 Resolution: 1.95→48.94 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2733 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: 28.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.94 Å
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Refine LS restraints |
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LS refinement shell |
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