+Open data
-Basic information
Entry | Database: PDB / ID: 4dbq | ||||||
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Title | MYOSIN VI D179Y (MD-INSERT2-CAM, DELTA-INSERT1) post-rigor state | ||||||
Components |
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Keywords | motor protein / calcium binding protein | ||||||
Function / homology | Function and homology information negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / negative regulation of opsin-mediated signaling pathway / photoreceptor cell axon guidance / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex ...negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / negative regulation of opsin-mediated signaling pathway / photoreceptor cell axon guidance / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex / regulation of secretion / kinetochore organization / autophagic cell death / centriole replication / G protein-coupled opsin signaling pathway / actin filament-based movement / inner ear auditory receptor cell differentiation / myosin V binding / cellular response to ethanol / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / muscle cell cellular homeostasis / mitotic spindle pole / myosin heavy chain binding / channel regulator activity / filamentous actin / cytoskeletal motor activity / microvillus / DNA damage response, signal transduction by p53 class mediator / enzyme regulator activity / clathrin-coated pit / ruffle / centriole / filopodium / actin filament organization / actin filament / sensory perception of sound / intracellular protein transport / ruffle membrane / mitotic spindle / ADP binding / actin filament binding / spindle / endocytosis / protein localization / sensory perception of smell / actin cytoskeleton / cell cortex / midbody / nuclear membrane / cytoplasmic vesicle / calmodulin binding / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Pylypenko, O. / Sweeney, H.L. / Houdusse, A. | ||||||
Citation | Journal: To be Published Title: Mutations in myosin VI that cause a loss of coordination between heads provide insights into the structural changes underlying force generation and the importance of gating Authors: Song, L. / Pylypenko, O. / Yang, Z. / Houdusse, A. / Sweeney, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dbq.cif.gz | 207.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dbq.ent.gz | 158.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dbq_validation.pdf.gz | 793.2 KB | Display | wwPDB validaton report |
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Full document | 4dbq_full_validation.pdf.gz | 805.9 KB | Display | |
Data in XML | 4dbq_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 4dbq_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/4dbq ftp://data.pdbj.org/pub/pdb/validation_reports/db/4dbq | 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 89947.562 Da / Num. of mol.: 1 Fragment: MOTOR DOMAIN-INSERT2, unp F1RQI7 residues 2-277, 304-815 Mutation: D179Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7, UniProt: Q29122*PLUS |
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#2: Protein | Mass: 16825.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62152 |
-Non-polymers , 6 types, 402 molecules
#3: Chemical | ChemComp-ADP / | ||||
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#4: Chemical | ChemComp-BEF / | ||||
#5: Chemical | ChemComp-MG / | ||||
#6: Chemical | #7: Chemical | ChemComp-CA / #8: 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: 3.33 Å3/Da / Density % sol: 63.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 50 mM Tris pH 8.5, 10% P8K, 1 mM TCEP, 6% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: Mar 17, 2009 |
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: 2.6→19.975 Å / Num. all: 44722 / Num. obs: 44526 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.6→2.7 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.975 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 22.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.734 Å2 / ksol: 0.298 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.975 Å
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Refine LS restraints |
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LS refinement shell |
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