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Yorodumi- PDB-2y9e: Structural basis for the allosteric interference of myosin functi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y9e | ||||||
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Title | Structural basis for the allosteric interference of myosin function by mutants G680A and G680V of Dictyostelium myosin-2 | ||||||
Components | MYOSIN-2 | ||||||
Keywords | MOTOR PROTEIN | ||||||
Function / homology | Function and homology information calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / myosin filament / filopodium assembly / myosin II complex / early phagosome / microfilament motor activity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to mechanical stimulus / response to cAMP / extracellular matrix / 14-3-3 protein binding / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.397 Å | ||||||
Authors | Preller, M. / Bauer, S. / Adamek, N. / Fujita-Becker, S. / Fedorov, R. / Geeves, M.A. / Manstein, D.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Basis for the Allosteric Interference of Myosin Function by Reactive Thiol Region Mutations G680A and G680V. Authors: Preller, M. / Bauer, S. / Adamek, N. / Fujita-Becker, S. / Fedorov, R. / Geeves, M.A. / Manstein, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y9e.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y9e.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 2y9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/2y9e ftp://data.pdbj.org/pub/pdb/validation_reports/y9/2y9e | HTTPS FTP |
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-Related structure data
Related structure data | 2y0rC 2y8iC 1mmdS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 86407.758 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 2-759 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / References: UniProt: P08799, EC: 3.6.4.1 |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 100 MM HEPES (PH 7.5), 20% PEG10000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9175 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9175 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→20 Å / Num. obs: 15092 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.34 |
Reflection shell | Resolution: 3.4→3.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.44 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MMD Resolution: 3.397→19.962 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 40.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.686 Å2 / ksol: 0.214 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.397→19.962 Å
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Refine LS restraints |
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LS refinement shell |
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