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Open data
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Basic information
Entry | Database: PDB / ID: 2bki | ||||||
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Title | Myosin VI nucleotide-free (MDinsert2-IQ) crystal structure | ||||||
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![]() | 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 | ![]() 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 / inner ear morphogenesis / microfilament motor activity / 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 / inner ear morphogenesis / microfilament motor activity / myosin binding / cytoskeletal motor activity / filamentous actin / microvillus / DNA damage response, signal transduction by p53 class mediator / endocytic vesicle / enzyme regulator activity / ruffle / filopodium / actin filament / actin filament organization / sensory perception of sound / intracellular protein transport / protein localization / ADP binding / ruffle membrane / endocytosis / disordered domain specific binding / actin filament binding / actin cytoskeleton / cell cortex / cytoplasmic vesicle / nuclear membrane / calmodulin binding / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Menetrey, J. / Bahloul, A. / Yengo, C. / Wells, A. / Morris, C. / Sweeney, H.L. / Houdusse, A. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.9 KB | Display | ![]() |
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PDB format | ![]() | 167.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.3 KB | Display | ![]() |
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Full document | ![]() | 483.6 KB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 49.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bkhC ![]() 1oe9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||||||
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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.) ![]() ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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