+Open data
-Basic information
Entry | Database: PDB / ID: 2bkh | ||||||
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Title | Myosin VI nucleotide-free (MDInsert2) crystal structure | ||||||
Components |
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Keywords | MOTOR PROTEIN/METAL-BINDING PROTEIN / COMPLEX (MOTOR PROTEIN-CALMODULIN) / MYOSIN VI / REVERSE MYOSIN / CALMODULIN / NON-CONVENTIONAL MYOSIN / NUCLEOTIDE-FREE CONFORMATION / MUSCLE PROTEIN / MOTOR PROTEIN-METAL-BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / deactivation of rhodopsin mediated signaling / rhabdomere / rhabdomere development / myosin V complex / : ...metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / deactivation of rhodopsin mediated signaling / rhabdomere / rhabdomere development / myosin V complex / : / regulation of secretion / kinetochore organization / adaptation of rhodopsin mediated signaling / actin filament-based movement / rhodopsin mediated signaling pathway / Neutrophil degranulation / inner ear auditory receptor cell differentiation / myosin V binding / channel regulator activity / vesicle transport along actin filament / cellular response to ethanol / myosin complex / clathrin-coated vesicle / microfilament motor activity / muscle cell cellular homeostasis / inner ear morphogenesis / myosin heavy chain binding / mitotic spindle pole / DNA damage response, signal transduction by p53 class mediator / filamentous actin / microvillus / centriole replication / cytoskeletal motor activity / enzyme regulator activity / ruffle / centriole / filopodium / actin filament organization / actin filament / ADP binding / sensory perception of sound / intracellular protein transport / spindle / endocytosis / mitotic spindle / ruffle membrane / actin filament binding / actin cytoskeleton / sensory perception of smell / cell cortex / midbody / cytoplasmic vesicle / nuclear membrane / vesicle / calmodulin binding / protein phosphorylation / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm 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. / Bahloul, A. / Yengo, C. / Wells, A. / Morris, C. / Sweeney, H.L. / Houdusse, A. | ||||||
Citation | Journal: Nature / Year: 2005 Title: The Structure of the Myosin Vi Motor Reveals the Mechanism of Directionality Reversal Authors: Menetrey, J. / Bahloul, A. / Wells, A. / Yengo, C. / Morris, C. / 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 | 2bkh.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bkh.ent.gz | 159.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bkh ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bkh | HTTPS FTP |
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-Related structure data
Related structure data | 2bkiC 1oe9S C: citing same article (ref.) S: Starting model for refinement |
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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: 93033.078 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN-INSERT2, RESIDUES 2-816 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / 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) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62152 | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | 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. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Details: 8-10% PEG 8000, 50MM MES PH 6.7, 150MM NH4.SO4, 3% ISO-PROPANOL, 3% TERT-BUTANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 49721 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE9 Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.454 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS 356-360 AND 623-639 IN CHAIN A AND 73-80 IN CHAIN B WERE NOT MODELED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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