[English] 日本語
Yorodumi- PDB-7ds6: Crystal structure of actin capping protein in complex with twinfl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ds6 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of actin capping protein in complex with twinflin-1/CD2AP CPI chimera peptide (TWN-CDC) | ||||||||||||
Components |
| ||||||||||||
Keywords | CYTOSOLIC PROTEIN / actin dynamics / actin capping protein / twinfilin / CARMIL / V-1 | ||||||||||||
Function / homology | Function and homology information 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 / negative regulation of small GTPase mediated signal transduction / Factors involved in megakaryocyte development and platelet production ...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 / negative regulation of small GTPase mediated signal transduction / Factors involved in megakaryocyte development and platelet production / transforming growth factor beta1 production / WASH complex / sperm connecting piece / F-actin capping protein complex / negative regulation of transforming growth factor beta1 production / negative regulation of filopodium assembly / response to transforming growth factor beta / sequestering of actin monomers / immunological synapse formation / substrate-dependent cell migration, cell extension / protein heterooligomerization / negative regulation of actin filament polymerization / cell junction assembly / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / podosome / regulation of cell morphogenesis / regulation of lamellipodium assembly / Nephrin family interactions / lamellipodium assembly / cortical cytoskeleton / myofibril / positive regulation of cardiac muscle hypertrophy / cell leading edge / filamentous actin / brush border / actin monomer binding / centriolar satellite / stress-activated MAPK cascade / cytoskeleton organization / ruffle / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / filopodium / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kidney development / actin filament organization / actin filament / positive regulation of protein secretion / regulation of actin cytoskeleton organization / synapse organization / protein catabolic process / neuromuscular junction / Schaffer collateral - CA1 synapse / cell morphogenesis / structural constituent of cytoskeleton / positive regulation of neuron projection development / fibrillar center / Z disc / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / actin filament binding / cell-cell junction / cell migration / actin cytoskeleton / late endosome / lamellipodium / actin binding / T cell receptor signaling pathway / actin cytoskeleton organization / protein-containing complex assembly / protein tyrosine kinase activity / vesicle / postsynaptic density / cadherin binding / cell cycle / inflammatory response / cell division / axon / dendrite / apoptotic process / protein-containing complex binding / perinuclear region of cytoplasm / signal transduction / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 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 | 7ds6.cif.gz | 145 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ds6.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ds6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/7ds6 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7ds6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7ds2SC 7ds3C 7ds4C 7ds8C 7dsaC 7dsbC 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/peptide | Mass: 2883.404 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: twinflin-1/CD2AP CPI chimera peptide (TWN-CDC),residues 315-327 of twinfilin-1 (UNP Q91YR1, KQHAHKQSFAK) were fused with residues 496-507 of CD2AP (UNP Q9Y5K6, MPGRRLPGRFNG) Source: (synth.) Mus musculus (house mouse), (synth.) Homo sapiens (human) References: UniProt: Q91YR1, UniProt: Q9Y5K6 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5% (w/v) PEG 3350, 5% (v/v) ethanol, 50mM Tris-HCl (pH = 7.0) |
-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: 1.69→48.07 Å / Num. obs: 54790 / % possible obs: 87.9 % / Redundancy: 5.703 % / Biso Wilson estimate: 27.928 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.093 / Χ2: 0.881 / Net I/σ(I): 14.58 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ds2 Resolution: 1.69→38.51 Å / SU ML: 0.2403 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0377 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: 26.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→38.51 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|