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Open data
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Basic information
Entry | Database: PDB / ID: 3aaa | ||||||
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Title | Crystal Structure of Actin capping protein in complex with V-1 | ||||||
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![]() | PROTEIN BINDING / ACTIN CAPPING PROTEIN / BARBED END CAPPING / INHIBITION / ACTIN CAPPING / ACTIN-BINDING / CYTOSKELETON / ANK REPEAT | ||||||
Function / homology | ![]() 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 / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / cerebellar granule cell differentiation ...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 / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / cerebellar granule cell differentiation / regulation of striated muscle tissue development / BRCA1-BARD1 complex / WASH complex / : / F-actin capping protein complex / BRCA1-A complex / negative regulation of filopodium assembly / skeletal muscle tissue regeneration / catecholamine metabolic process / protein K6-linked ubiquitination / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / regulation of cell size / cortical cytoskeleton / positive regulation of cardiac muscle hypertrophy / brush border / cytoskeleton organization / striated muscle cell differentiation / positive regulation of protein metabolic process / hippocampal mossy fiber to CA3 synapse / Schaffer collateral - CA1 synapse / cell morphogenesis / neuron differentiation / Z disc / cellular response to mechanical stimulus / ubiquitin-protein transferase activity / actin filament binding / lamellipodium / regulation of translation / positive regulation of NF-kappaB transcription factor activity / actin cytoskeleton organization / positive regulation of cell growth / sequence-specific DNA binding / postsynaptic density / axon / perinuclear region of cytoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takeda, S. / Minakata, S. / Narita, A. / Kitazawa, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y. | ||||||
![]() | ![]() Title: Two distinct mechanisms for actin capping protein regulation--steric and allosteric inhibition Authors: Takeda, S. / Minakata, S. / Koike, R. / Kawahata, I. / Narita, A. / Kitazawa, M. / Ota, M. / Yamakuni, T. / Maeda, Y. / Nitanai, 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 | ![]() | 145.6 KB | Display | ![]() |
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PDB format | ![]() | 112.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.6 KB | Display | ![]() |
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Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aa0C ![]() 3aa1C ![]() 3aa6C ![]() 3aa7C ![]() 1iznS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THE ORIGOMETRIC STATE OF THE ACTIN CAPPING PROTEIN IS A HETERO DIMER COMPOSE OF SUBUNIT A (CHAIN A) AND SUBUNIT B (CHAIN B) IN VIVO AND IN VITRO. |
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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: 31403.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Protein | Mass: 13324.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.35 Details: 10% PEG 4000, 20% ISOPROPANOL, 20MM EDTA, 0.1M TRIS-HCL, pH 8.35, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 14, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 38745 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 24.62 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 7.68 / Num. unique all: 3818 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IZN Resolution: 2.2→19.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.813 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.226 Å2
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Refine analyze | Luzzati coordinate error obs: 0.238 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.205→2.261 Å / Total num. of bins used: 20
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