[English] 日本語
Yorodumi- PDB-7dsb: Crystal structure of actin capping protein in complex with V-1 an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dsb | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of actin capping protein in complex with V-1 and twinfilin C-terminal tail | ||||||||||||
Components |
| ||||||||||||
Keywords | CYTOSOLIC PROTEIN / actin dynamics / actin capping protein / twinfilin / CARMIL / V-1 | ||||||||||||
Function / homology | Function and homology information positive regulation of macromolecule biosynthetic process / regulation of barbed-end actin filament capping / : / 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 / : / 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 / WASH complex / : / F-actin capping protein complex / negative regulation of filopodium assembly / sequestering of actin monomers / skeletal muscle tissue regeneration / negative regulation of actin filament polymerization / catecholamine metabolic process / 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 / 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 / cellular response to mechanical stimulus / cell morphogenesis / Schaffer collateral - CA1 synapse / neuron differentiation / Z disc / positive regulation of neuron projection development / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / regulation of translation / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protein tyrosine kinase activity / actin cytoskeleton organization / 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 | Gallus gallus (chicken) Homo sapiens (human) Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 Å | ||||||||||||
Authors | Takeda, S. | ||||||||||||
Funding support | Japan, 3items
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dsb.cif.gz | 154 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dsb.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dsb_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7dsb_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 7dsb_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 7dsb_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/7dsb ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7dsb | HTTPS FTP |
-Related structure data
Related structure data | 7ds2C 7ds3C 7ds4C 7ds6C 7ds8C 7dsaC 3aaaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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 |
---|---|
#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 | Mass: 13324.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTPN / Production host: Escherichia coli (E. coli) / References: UniProt: P58546 |
#4: Protein/peptide | Mass: 3331.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q91YR1 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|