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Yorodumi- PDB-1c0f: CRYSTAL STRUCTURE OF DICTYOSTELIUM CAATP-ACTIN IN COMPLEX WITH GE... -
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-Basic information
Entry | Database: PDB / ID: 1c0f | ||||||
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Title | CRYSTAL STRUCTURE OF DICTYOSTELIUM CAATP-ACTIN IN COMPLEX WITH GELSOLIN SEGMENT 1 | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / CA ACTIN | ||||||
Function / homology | Function and homology information RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / intranuclear rod / Platelet degranulation / Regulation of actin dynamics for phagocytic cup formation / phototaxis / leading edge of lamellipodium / phagolysosome / macropinocytic cup / cell pole ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / intranuclear rod / Platelet degranulation / Regulation of actin dynamics for phagocytic cup formation / phototaxis / leading edge of lamellipodium / phagolysosome / macropinocytic cup / cell pole / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / plasma membrane repair / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / early phagosome / cardiac muscle cell contraction / hyperosmotic response / podosome / sarcoplasm / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / phagocytic cup / phagocytosis, engulfment / myosin binding / cortical actin cytoskeleton / hepatocyte apoptotic process / cell leading edge / pseudopodium / mitotic cytokinesis / endocytic vesicle / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phagocytosis / response to cAMP / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / lipid droplet / central nervous system development / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cell morphogenesis / structural constituent of cytoskeleton / cellular response to type II interferon / endocytosis / chemotaxis / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / actin binding / cell cortex / blood microparticle / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / hydrolase activity / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Matsuura, Y. / Stewart, M. / Kawamoto, M. / Kamiya, N. / Saeki, K. / Yasunaga, T. / Wakabayashi, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structural basis for the higher Ca(2+)-activation of the regulated actin-activated myosin ATPase observed with Dictyostelium/Tetrahymena actin chimeras Authors: Matsuura, Y. / Stewart, M. / Kawamoto, M. / Kamiya, N. / Saeki, K. / Yasunaga, T. / Wakabayashi, T. #1: Journal: Nature / Year: 1993 Title: Structure of gelsolin segment 1-actin complex and the mechanism of filament severing Authors: McLaughlin, P.J. / Gooch, J.T. / Mannherz, H.G. / Weeds, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c0f.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c0f.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 1c0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/1c0f ftp://data.pdbj.org/pub/pdb/validation_reports/c0/1c0f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14205.001 Da / Num. of mol.: 1 / Mutation: N35C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06396 | ||||
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#2: Protein | Mass: 40957.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P07830 | ||||
#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: IMIDAZOLE, SODIUM CHLORIDE, ATP, CALCIUM CHLORIDE, MAGNESIUM CHLORIDE, SODIUM AZIDE, DITHIOTHREITOL, PEG 6000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.1 Å / Num. obs: 27962 / % possible obs: 94.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.4→2.52 Å / Rmerge(I) obs: 0.155 |
Reflection | *PLUS % possible obs: 94.9 % / Num. measured all: 68469 |
Reflection shell | *PLUS Mean I/σ(I) obs: 4.5 |
-Processing
Software |
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Refinement | Resolution: 2.4→10 Å / Cross valid method: THROUGHOUT /
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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