+Open data
-Basic information
Entry | Database: PDB / ID: 2vas | ||||||
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Title | Myosin VI (MD-insert2-CaM, Delta-Insert1) Post-rigor state | ||||||
Components |
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Keywords | MOTOR PROTEIN / CALMODULIN-BINDING / NUCLEOTIDE-BINDING / TRANSPORT / CALMODULIN / ENDOCYTOSIS / MG.ADP.BEFX / CAM / MYOSIN / NUCLEUS / MEMBRANE / MYOSIN VI / CYTOPLASM / GOLGI APPARATUS / PHOSPHORYLATION / MOLECULAR MOTOR / ATP-BINDING / COILED COIL / ACTIN-BINDING / POST-RIGOR STATE / PROTEIN TRANSPORT | ||||||
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 / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / 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 / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex / regulation of secretion / kinetochore organization / autophagic cell death / : / G protein-coupled opsin signaling pathway / actin filament-based movement / inner ear auditory receptor cell differentiation / myosin V binding / vesicle transport along actin filament / channel regulator activity / cellular response to ethanol / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / muscle cell cellular homeostasis / microfilament motor activity / mitotic spindle pole / myosin heavy chain binding / cytoskeletal motor activity / filamentous actin / centriole replication / microvillus / DNA damage response, signal transduction by p53 class mediator / endocytic vesicle / enzyme regulator activity / ruffle / centriole / filopodium / actin filament / actin filament organization / sensory perception of sound / intracellular protein transport / protein localization / mitotic spindle / ADP binding / ruffle membrane / spindle / endocytosis / actin filament binding / sensory perception of smell / actin cytoskeleton / cell cortex / midbody / cytoplasmic vesicle / nuclear membrane / calmodulin binding / protein phosphorylation / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Menetrey, J. / Llinas, P. / Cicolari, J. / Squires, G. / Liu, X. / Li, A. / Sweeney, H.L. / Houdusse, A. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: The Post-Rigor Structure of Myosin Vi and Implications for the Recovery Stroke. Authors: Menetrey, J. / Llinas, P. / Cicolari, J. / Squires, G. / Liu, X. / Li, A. / 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 | 2vas.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vas.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vas_validation.pdf.gz | 807.8 KB | Display | wwPDB validaton report |
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Full document | 2vas_full_validation.pdf.gz | 820.6 KB | Display | |
Data in XML | 2vas_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 2vas_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2vas ftp://data.pdbj.org/pub/pdb/validation_reports/va/2vas | HTTPS FTP |
-Related structure data
Related structure data | 2vb6C 2bkhS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 89899.477 Da / Num. of mol.: 1 Fragment: MOTOR DOMAIN-INSERT2,RESIDUES 2-277,304-377,379-816 Source method: isolated from a genetically manipulated source Details: INSERT1 DELETION (C278-A303) / Source: (gene. exp.) SUS SCROFA (pig) / Plasmid: SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122 |
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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) / Plasmid: SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62152 |
-Non-polymers , 5 types, 161 molecules
#3: Chemical | ChemComp-ADP / | ||
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#4: Chemical | ChemComp-BEF / | ||
#5: Chemical | ChemComp-MG / | ||
#6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY ...THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY INCORRECT BECAUSE THE CHANGES THAT ARE IN THEIR CLONE (LYS DELETION AND THE 6 MUTATIONS) ARE CONSERVED ACROSS THE MYOSIN VI FAMILY. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 53.1 % / Description: NONE |
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Crystal grow | Details: 8% PEG 8000, 50MM GLYCINE PH 9.5, 6% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 29, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.97 Å / Num. obs: 51218 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BKH Resolution: 2.4→48.28 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.393 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→48.28 Å
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