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Yorodumi- PDB-4pjk: Dicty myosin II R238E.E459R mutant (with ADP.Pi) in the Pi releas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pjk | ||||||||||||
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Title | Dicty myosin II R238E.E459R mutant (with ADP.Pi) in the Pi release state | ||||||||||||
Components | Myosin-2 heavy chain | ||||||||||||
Keywords | MOTOR PROTEIN / MOTOR DOMAIN MUTANT | ||||||||||||
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 / contractile actin filament bundle assembly / cell trailing edge ...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 / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / 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 / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / myosin II complex / cortical actin cytoskeleton organization / microfilament motor activity / cortical actin cytoskeleton / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / cell motility / response to hydrogen peroxide / actin filament binding / chemotaxis / protein localization / regulation of cell shape / cell cortex / cytoplasmic vesicle / calmodulin binding / cytoskeleton / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||||||||
Authors | Isabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
Funding support | France, United States, 3items
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Citation | Journal: Dev.Cell / Year: 2015 Title: How actin initiates the motor activity of Myosin. Authors: Llinas, P. / Isabet, T. / Song, L. / Ropars, V. / Zong, B. / Benisty, H. / Sirigu, S. / Morris, C. / Kikuti, C. / Safer, D. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pjk.cif.gz | 307.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pjk.ent.gz | 244.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pjk_validation.pdf.gz | 821.6 KB | Display | wwPDB validaton report |
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Full document | 4pjk_full_validation.pdf.gz | 824.6 KB | Display | |
Data in XML | 4pjk_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 4pjk_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/4pjk ftp://data.pdbj.org/pub/pdb/validation_reports/pj/4pjk | HTTPS FTP |
-Related structure data
Related structure data | 4pfoC 4pfpC 4pjjC 4pjlC 4pjmC 4pjnC 4pk4C 1vomS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 87779.164 Da / Num. of mol.: 1 / Mutation: R238E, E459R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA, DDB_G0286355 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08799, EC: 3.6.4.1 |
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-Non-polymers , 5 types, 391 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-ADP / | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 11,25% PEG8k, 100mM MOPS pH 7,5, 1mM TCEP, 250mM MgCl2, 50mM NaH2PO4 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2010 |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 55100 / % possible obs: 99.9 % / Redundancy: 7.41 % / Biso Wilson estimate: 44.17 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 12.64 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 4.99 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1.79 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VOM Resolution: 2.15→43.55 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.152
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Displacement parameters | Biso mean: 54.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.286 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→43.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.8624 Å / Origin y: -37.3209 Å / Origin z: 29.2205 Å
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Refinement TLS group | Selection details: { A|* } |