[English] 日本語
Yorodumi- PDB-2y65: Crystal structure of Drosophila melanogaster kinesin-1 motor doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y65 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Drosophila melanogaster kinesin-1 motor domain dimer-tail complex | ||||||
Components | (KINESIN HEAVY CHAIN) x 2 | ||||||
Keywords | MOTOR PROTEIN | ||||||
Function / homology | Function and homology information : / actin filament bundle organization / anterograde axonal transport of mitochondrion / anterograde dendritic transport / mitochondrion distribution / larval locomotory behavior / oocyte microtubule cytoskeleton polarization / 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 / mitochondrion distribution / larval locomotory behavior / oocyte microtubule cytoskeleton polarization / 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 / larval somatic muscle development / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / transport along microtubule / centrosome separation / anterograde dendritic transport of neurotransmitter receptor complex / actin cap / microtubule plus-end / plus-end-directed microtubule motor activity / axo-dendritic transport / stress granule disassembly / nuclear migration / dendrite morphogenesis / kinesin complex / synaptic vesicle transport / microtubule motor activity / tropomyosin binding / intracellular distribution of mitochondria / microtubule-based movement / microtubule polymerization / cytoskeletal motor activity / axon cytoplasm / dendrite cytoplasm / axonogenesis / axon guidance / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2y65.cif.gz | 301.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2y65.ent.gz | 243.6 KB | Display | PDB format |
PDBx/mmJSON format | 2y65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y65 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y65 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2y5wSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9805, 0.0458, -0.1911), Vector: Details | OWING TO ITS AMINO ACID SEQUENCE, CHAINS X AND Y ARE ALMOST SYMMETRICAL, IN TERMS OF SIDE CHAIN PROPERTIES, ABOUT THE LYS 944 RESIDUE. THIS DISTINCTIVE FEATURE OF THE CHAINS X AND Y ALLOWS THEM TO BIND IN TWO DIRECTIONS BETWEEN THE DIMERS A-A' AND B-B', WHICH ALSO EXHIBIT TWO-FOLD SYMMETRY. | |
-Components
#1: Protein | Mass: 40885.301 Da / Num. of mol.: 4 / 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: Protein/peptide | Mass: 1913.098 Da / Num. of mol.: 3 / Fragment: TAIL DOMAIN RESIDUES 937-952 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17210 #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % / Description: NONE |
---|---|
Crystal grow | pH: 7.4 Details: 18% POLYETHYLENE GLYCOL-3350, 0.2M POTASSIUM CHLORIDE, 0.1M HEPES SODIUM PH 7.4 |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 80517 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 41.383 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.5 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y5W Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.611 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PSEUDOSYMMETRY IN THE CRYSTAL STRUCTURE, WHERE CHAINS X AND Y LIE ON THE TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 42.405 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|