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Yorodumi- PDB-6z7u: Myosin-II motor domain complexed with blebbistatin in a new ADP-r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z7u | ||||||
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Title | Myosin-II motor domain complexed with blebbistatin in a new ADP-release conformation | ||||||
Components | Myosin-2 heavy chain | ||||||
Keywords | MOTOR PROTEIN / myosin / motorprotein / blebbistatin / ADP-release / inhibitor / complex / hydrolase | ||||||
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: 2.58 Å | ||||||
Authors | Ewert, W. / Preller, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Int J Mol Sci / Year: 2020 Title: Structural and Computational Insights into a Blebbistatin-Bound Myosin•ADP Complex with Characteristics of an ADP-Release Conformation along the Two-Step Myosin Power Stoke. Authors: Ewert, W. / Franz, P. / Tsiavaliaris, G. / Preller, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z7u.cif.gz | 297.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z7u.ent.gz | 235.4 KB | Display | PDB format |
PDBx/mmJSON format | 6z7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/6z7u ftp://data.pdbj.org/pub/pdb/validation_reports/z7/6z7u | HTTPS FTP |
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-Related structure data
Related structure data | 6z7tC 2akaS S: Starting model for refinement C: citing same article (ref.) |
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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: 88724.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA, DDB_G0286355 / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799 | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-BIT / (-)- | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, pH7.5, 10% PEG8000, 8% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→46.1 Å / Num. obs: 27424 / % possible obs: 99.92 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.78 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.41 |
Reflection shell | Resolution: 2.58→2.67 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 2669 / CC1/2: 0.754 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2aka Resolution: 2.58→46.1 Å / SU ML: 0.3362 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 26.598 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→46.1 Å
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Refine LS restraints |
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LS refinement shell |
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