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- PDB-3aa6: Crystal structure of Actin capping protein in complex with the Cp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3aa6 | ||||||
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Title | Crystal structure of Actin capping protein in complex with the Cp-binding motif derived from CD2AP | ||||||
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![]() | PROTEIN BINDING / ACTIN CAPPING PROTEIN / BARBED END REGULATION / CARMIL FAMILY PROTEIN / CONFORMATIONAL CHANGE / CELL MOTILITY / CD2AP / Actin capping / Actin-binding / Cytoskeleton / Cell cycle / Cell division / Cell projection / Mitosis / SH3 domain / SH3-binding | ||||||
Function / homology | ![]() 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 / 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 ...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 / 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 / nerve growth factor signaling pathway / cell-cell adhesion mediated by cadherin / collateral sprouting / protein heterooligomerization / renal albumin absorption / substrate-dependent cell migration, cell extension / membrane organization / cell junction assembly / phosphatidylinositol 3-kinase regulatory subunit binding / 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 / cortical cytoskeleton / maintenance of blood-brain barrier / nuclear envelope lumen / cell leading edge / glucose import / filamentous actin / brush border / neurotrophin TRK receptor signaling pathway / centriolar satellite / protein secretion / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / cytoskeleton organization / 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 / positive regulation of protein secretion / 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 / Z disc / response to wounding / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / actin filament binding / cell migration / actin cytoskeleton / late endosome / lamellipodium / T cell receptor signaling pathway / growth cone / actin cytoskeleton organization / protein-containing complex assembly / vesicle / response to oxidative stress / negative regulation of neuron apoptotic process / cell population proliferation / postsynaptic density / inflammatory response / cadherin binding / cell cycle / cell division / axon 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 | ![]() | 132.9 KB | Display | ![]() |
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PDB format | ![]() | 101.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.7 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aa0C ![]() 3aa1C ![]() 3aa7C ![]() 3aaaC ![]() 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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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: 27473.070 Da / Num. of mol.: 1 / Mutation: residues 244-277 deletion mutation Source method: isolated from a genetically manipulated source Details: BETA TENTACLE DELETION / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 2622.107 Da / Num. of mol.: 1 / Fragment: recidues 485-507 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) ![]() |
#4: Chemical | ChemComp-BA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% PEG 400, 20MM BACL2, 100MM MES-NAOH, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 10, 2009 / 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: 1.9→50 Å / Num. obs: 41167 / % possible obs: 96 % / Redundancy: 6.6 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.43 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.71 / Num. unique all: 3026 / % possible all: 71.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IZN Resolution: 1.9→45.311 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.502 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.164 / 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: 24.624 Å2
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Refine analyze | Luzzati coordinate error obs: 0.195 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.311 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Total num. of bins used: 20
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