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Yorodumi- PDB-1dej: CRYSTAL STRUCTURE OF A DICTYOSTELIUM/TETRAHYMENA CHIMERA ACTIN (M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dej | ||||||
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Title | CRYSTAL STRUCTURE OF A DICTYOSTELIUM/TETRAHYMENA CHIMERA ACTIN (MUTANT 646: Q228K/T229A/A230Y/A231K/S232E/E360H) IN COMPLEX WITH HUMAN GELSOLIN SEGMENT 1 | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / ACTIN MUTANT | ||||||
Function / homology | Function and homology information intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption ...intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / 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 cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cell pole / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / plasma membrane repair / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / early phagosome / hyperosmotic response / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cortical actin cytoskeleton / myosin binding / phagocytosis, engulfment / hepatocyte apoptotic process / cell leading edge / pseudopodium / phagocytic cup / mitotic cytokinesis / endocytic vesicle / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / vesicle-mediated transport / phagocytic vesicle / response to cAMP / 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 / actin filament binding / endocytosis / chemotaxis / cell-cell junction / actin cytoskeleton / lamellipodium / actin binding / cell cortex / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Dictyostelium discoideum (eukaryote) Tetrahymena thermophila (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. #2: Journal: Biochemistry / Year: 1996 Title: Tropomyosin Binding Site(S) on the Dictyostelium Actin Surface as Identified by Site-Directed Mutagenesis Authors: Saeki, K. / Sutoh, K. / Wakabayashi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dej.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dej.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dej_validation.pdf.gz | 725.9 KB | Display | wwPDB validaton report |
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Full document | 1dej_full_validation.pdf.gz | 735.6 KB | Display | |
Data in XML | 1dej_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 1dej_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1dej ftp://data.pdbj.org/pub/pdb/validation_reports/de/1dej | HTTPS FTP |
-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 / Fragment: SEGMENT 1 / Mutation: YES 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: 41832.715 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum, Tetrahymena thermophila Genus: Dictyostelium, Tetrahymena / Species: , / Strain: , / Production host: 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: 3.23 Å3/Da / Density % sol: 61.87 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, NACL, CACL2, MGCL2, ATP, PEG6000, DTT, NAN3, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
Detector | Type: OTHER / Detector: IMAGE PLATE / Date: Jun 29, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 96715 / % possible obs: 93.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.055 / % possible all: 88.1 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. obs: 27352 / Num. measured all: 96715 |
Reflection shell | *PLUS Mean I/σ(I) obs: 19.3 |
-Processing
Software |
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Refinement | Resolution: 2.4→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.171 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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