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- PDB-2y5w: Crystal structure of Drosophila melanogaster kinesin-1 motor doma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y5w | ||||||
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Title | Crystal structure of Drosophila melanogaster kinesin-1 motor domain dimer | ||||||
![]() | KINESIN HEAVY CHAIN | ||||||
![]() | MOTOR PROTEIN / MICROTUBULE ASSOCIATED / ATPASE | ||||||
Function / homology | ![]() actin filament bundle organization / anterograde axonal transport of mitochondrion / anterograde dendritic transport / ovarian nurse cell to oocyte transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / larval locomotory behavior / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization ...actin filament bundle organization / anterograde axonal transport of mitochondrion / anterograde dendritic transport / ovarian nurse cell to oocyte transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / larval locomotory behavior / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / pole plasm assembly / microtubule sliding / dorsal appendage formation / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / larval somatic muscle development / transport along microtubule / centrosome separation / anterograde dendritic transport of neurotransmitter receptor complex / actin cap / microtubule plus-end / axo-dendritic transport / plus-end-directed microtubule motor activity / nuclear migration / stress granule disassembly / dendrite morphogenesis / microtubule motor activity / kinesin complex / synaptic vesicle transport / tropomyosin binding / microtubule-based movement / intracellular distribution of mitochondria / cytoskeletal motor activity / microtubule polymerization / axon cytoplasm / dendrite cytoplasm / axonogenesis / axon guidance / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kaan, H.Y.K. / Hackney, D.D. / Kozielski, F. | ||||||
![]() | ![]() Title: The Structure of the Kinesin-1 Motor-Tail Complex Reveals the Mechanism of Autoinhibition. Authors: Kaan, H.Y.K. / Hackney, D.D. / Kozielski, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.3 KB | Display | ![]() |
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PDB format | ![]() | 114.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2y65C ![]() 1bg2S 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: 40885.301 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 1-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.44 % / Description: NONE |
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Crystal grow | pH: 7.8 Details: 24 % POLYETHYLENE GLYCOL-3350, 0.15 M AMMONIUM SULFATE, AND 0.1 M HEPES SODIUM PH 7.8 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 35890 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 55.874 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.7→2.84 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BG2 Resolution: 2.7→29.74 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.502 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.664 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 40.125 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→29.74 Å
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Refine LS restraints |
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