[English] 日本語
Yorodumi- PDB-4pxu: Structural basis for the assembly of the mitotic motor kinesin-5 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pxu | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis for the assembly of the mitotic motor kinesin-5 into bipolar tetramers | ||||||
Components | Bipolar kinesin KRP-130 | ||||||
Keywords | CELL CYCLE / Coiled-coil / Bipolar assembly domain of kinesin-5 / bipolar tetramers / anti-parallel four-helix bundle / Kinesin-5 functions via a "sliding filament" mechanism / crosslinking adjacent microtubules into bundles throughout the mitotic spindle / Microtubules | ||||||
Function / homology | Function and homology information aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / microtubule bundle formation ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / microtubule bundle formation / positive regulation of Golgi to plasma membrane protein transport / plus-end-directed microtubule motor activity / mitotic centrosome separation / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / protein secretion / mitotic spindle assembly / mitotic spindle organization / spindle microtubule / mitotic spindle / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å | ||||||
Authors | Scholey, J.E. / Nithianantham, S. / Scholey, J.M. / Al-Bassam, J. | ||||||
Citation | Journal: Elife / Year: 2014 Title: Structural basis for the assembly of the mitotic motor Kinesin-5 into bipolar tetramers. Authors: Scholey, J.E. / Nithianantham, S. / Scholey, J.M. / Al-Bassam, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pxu.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pxu.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pxu_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4pxu_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 4pxu_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4pxu_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/4pxu ftp://data.pdbj.org/pub/pdb/validation_reports/px/4pxu | HTTPS FTP |
-Related structure data
Related structure data | 4pxtSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24233.400 Da / Num. of mol.: 2 / Fragment: Bipolar assembly domain of kinesin-5 (Klp61f) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: Drosophila melanogaster / Gene: CG9191, KLP2, Klp61F, Klp61F or DmKlp61F or CG9191 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46863 #2: Chemical | ChemComp-MPD / ( | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 4-6 % (+/-) 2-Methyl-2,4 pentanediol (MPD), 100mM MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 6-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013 / Details: K-B focusing mirrors |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.601→40.024 Å / Num. all: 18960 / Num. obs: 15885 / % possible obs: 83.84 % / Observed criterion σ(F): 1.36 / Observed criterion σ(I): 2.3 / Redundancy: 8.2 % / Biso Wilson estimate: 75.9 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.111 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2694 / Rsym value: 0.966 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4PXT Resolution: 2.601→40.024 Å / SU ML: 0.31 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 2.3 / Phase error: 30.36 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.55 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.601→40.024 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|