+Open data
-Basic information
Entry | Database: PDB / ID: 2bki | ||||||
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Title | Myosin VI nucleotide-free (MDinsert2-IQ) crystal structure | ||||||
Components |
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Keywords | MOTOR PROTEIN/METAL-BINDING PROTEIN / MOTOR PROTEIN-METAL-BINDING PROTEIN COMPLEX / COMPLEX (MOTOR PROTEIN-CALMODULIN) / MYOSIN VI / REVERSE MYOSIN / CALMODULIN / IQ MOTIF / NON- CONVENTIONAL MYOSIN / NUCLEOTIDE-FREE CONFORMATION / MUSCLE PROTEIN | ||||||
Function / homology | Function and homology information CH domain binding / regulation of secretion / actin filament-based movement / inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / microfilament motor activity / inner ear morphogenesis / myosin binding ...CH domain binding / regulation of secretion / actin filament-based movement / inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / microfilament motor activity / inner ear morphogenesis / myosin binding / filamentous actin / microvillus / cytoskeletal motor activity / DNA damage response, signal transduction by p53 class mediator / ruffle / filopodium / actin filament organization / actin filament / ADP binding / sensory perception of sound / intracellular protein transport / ruffle membrane / endocytosis / disordered domain specific binding / actin filament binding / actin cytoskeleton / cell cortex / cytoplasmic vesicle / nuclear membrane / vesicle / calmodulin binding / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 2bki.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bki.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bki ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bki | HTTPS FTP |
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-Related structure data
Related structure data | 2bkhC 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: 98285.633 Da / Num. of mol.: 1 / Fragment: DOMAIN LONG-S1, RESIDUES 1-858 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122 | ||||||||
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#2: Protein | Mass: 16852.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62149 #3: Chemical | ChemComp-SO4 / | #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: 3.91 Å3/Da / Density % sol: 68.31 % |
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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: ID23-1 / Wavelength: 0.96115 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96115 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. obs: 38961 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.9→3.06 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE9 Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.809 / SU B: 17.988 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 1.125 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CAM BOUND TO THE IQ MOTIF IS POORLY DEFINED IN THE DENSITY, ONLY POLY-ALA CHAINS HAVE BEEN MODELED FOR IT.
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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: 43.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→40 Å
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Refine LS restraints |
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