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- PDB-7ds6: Crystal structure of actin capping protein in complex with twinfl... -
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Basic information
Entry | Database: PDB / ID: 7ds6 | ||||||||||||
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Title | Crystal structure of actin capping protein in complex with twinflin-1/CD2AP CPI chimera peptide (TWN-CDC) | ||||||||||||
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![]() | CYTOSOLIC PROTEIN / actin dynamics / actin capping protein / twinfilin / CARMIL / V-1 | ||||||||||||
Function / homology | ![]() 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 / response to glial cell derived neurotrophic factor / RHOBTB2 GTPase cycle / COPI-mediated anterograde transport / negative regulation of small GTPase mediated signal transduction ...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 / response to glial cell derived neurotrophic factor / 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 / localization of cell / Rab protein signal transduction / WASH complex / : / F-actin capping protein complex / negative regulation of transforming growth factor beta1 production / slit diaphragm / negative regulation of filopodium assembly / response to transforming growth factor beta / podocyte differentiation / immunological synapse formation / endothelium development / sequestering of actin monomers / nerve growth factor signaling pathway / cell-cell adhesion mediated by cadherin / collateral sprouting / protein heterooligomerization / negative regulation of actin filament polymerization / renal albumin absorption / substrate-dependent cell migration, cell extension / membrane organization / cell junction assembly / phosphatidylinositol 3-kinase regulatory subunit binding / actin filament depolymerization / cell-cell junction organization / filopodium assembly / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / podosome / regulation of lamellipodium assembly / Nephrin family interactions / lamellipodium assembly / clathrin binding / myofibril / cortical cytoskeleton / maintenance of blood-brain barrier / nuclear envelope lumen / positive regulation of cardiac muscle hypertrophy / cell leading edge / glucose import / filamentous actin / brush border / neurotrophin TRK receptor signaling pathway / centriolar satellite / protein secretion / actin monomer binding / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding / ERK1 and ERK2 cascade / hippocampal mossy fiber to CA3 synapse / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / trans-Golgi network membrane / liver development / filopodium / positive regulation of protein secretion / actin filament / regulation of actin cytoskeleton organization / actin filament organization / synapse organization / Schaffer collateral - CA1 synapse / protein catabolic process / response to virus / response to insulin / regulation of synaptic plasticity / neuromuscular junction / cell morphogenesis / lipid metabolic process / structural constituent of cytoskeleton / fibrillar center / positive regulation of neuron projection development / Z disc / response to wounding / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / cell-cell junction / actin filament binding / cell migration / actin cytoskeleton / late endosome / lamellipodium / T cell receptor signaling pathway 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 | ![]() | 145 KB | Display | ![]() |
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PDB format | ![]() | 101.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 446 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ds2SC ![]() 7ds3C ![]() 7ds4C ![]() 7ds8C ![]() 7dsaC ![]() 7dsbC 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/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.) ![]() ![]() ![]() References: UniProt: Q91YR1, UniProt: Q9Y5K6 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.43 % |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 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
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: 26.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→38.51 Å
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Refine LS restraints |
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LS refinement shell |
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