+Open data
-Basic information
Entry | Database: PDB / ID: 3vkh | |||||||||
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Title | X-ray structure of a functional full-length dynein motor domain | |||||||||
Components | Dynein heavy chain, cytoplasmic | |||||||||
Keywords | MOTOR PROTEIN / AAA+ protein / molecular motor / microtubles | |||||||||
Function / homology | Function and homology information minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding ...minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / microtubule motor activity / dynein intermediate chain binding / ATPase complex / endocytic vesicle / mitotic spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / cell cortex / microtubule binding / microtubule / centrosome / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Dictyostelium discoideum (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | |||||||||
Authors | Kon, T. / Oyama, T. / Shimo-Kon, R. / Suto, K. / Kurisu, G. | |||||||||
Citation | Journal: Nature / Year: 2012 Title: The 2.8 A crystal structure of the dynein motor domain Authors: Kon, T. / Oyama, T. / Shimo-Kon, R. / Imamula, K. / Shima, T. / Sutoh, K. / Kurisu, G. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: X-ray structure of a functional full-length dynein motor domain. Authors: Kon, T. / Sutoh, K. / Kurisu, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vkh.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3vkh.ent.gz | 859.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/3vkh ftp://data.pdbj.org/pub/pdb/validation_reports/vk/3vkh | HTTPS FTP |
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-Related structure data
Related structure data | 3vkgSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 384331.344 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1388-4730 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0276355, dhcA / Plasmid: PHSG3MB38HFG380 / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P34036 #2: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3.0-6.0% PEG 8000, 10MM SPERMINE-HCL, 3MM ADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 25, 2011 / Details: mirror |
Radiation | Monochromator: SI 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→150 Å / Num. obs: 88890 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 31.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VKG Resolution: 3.8→48.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 9102566.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 85.7688 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 138.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.8→48.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→4.04 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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