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Yorodumi- PDB-2y5w: Crystal structure of Drosophila melanogaster kinesin-1 motor doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y5w | ||||||
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Title | Crystal structure of Drosophila melanogaster kinesin-1 motor domain dimer | ||||||
Components | KINESIN HEAVY CHAIN | ||||||
Keywords | MOTOR PROTEIN / MICROTUBULE ASSOCIATED / ATPASE | ||||||
Function / homology | Function and homology information 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 | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Kaan, H.Y.K. / Hackney, D.D. / Kozielski, F. | ||||||
Citation | Journal: Science / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y5w.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y5w.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 2y5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y5w_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2y5w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2y5w_validation.xml.gz | 30 KB | Display | |
Data in CIF | 2y5w_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y5w ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y5w | HTTPS FTP |
-Related structure data
Related structure data | 2y65C 1bg2S 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: 40885.301 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 1-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: P17210 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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