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- PDB-3vhx: The crystal structure of Arf6-MKLP1 (Mitotic kinesin-like protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vhx | ||||||
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Title | The crystal structure of Arf6-MKLP1 (Mitotic kinesin-like protein 1) complex | ||||||
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![]() | CELL CYCLE/SIGNALING PROTEIN / Small GTPase / GTP Binding / Flemming body / Cytokinesis / CELL CYCLE-SIGNALING PROTEIN complex | ||||||
Function / homology | ![]() centralspindlin complex / TBC/RABGAPs / MET receptor recycling / actomyosin contractile ring assembly / maintenance of postsynaptic density structure / plus-end-directed vesicle transport along microtubule / myeloid cell apoptotic process / Mitotic Telophase/Cytokinesis / mitotic spindle midzone assembly / mitotic spindle elongation ...centralspindlin complex / TBC/RABGAPs / MET receptor recycling / actomyosin contractile ring assembly / maintenance of postsynaptic density structure / plus-end-directed vesicle transport along microtubule / myeloid cell apoptotic process / Mitotic Telophase/Cytokinesis / mitotic spindle midzone assembly / mitotic spindle elongation / : / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / regulation of toll-like receptor 4 signaling pathway / negative regulation of dendrite development / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / Clathrin-mediated endocytosis / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / thioesterase binding / endocytic recycling / filopodium membrane / Flemming body / Kinesins / protein localization to cell surface / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / cortical actin cytoskeleton organization / regulation of neuron projection development / kinesin complex / intercellular bridge / positive regulation of actin filament polymerization / microtubule-based movement / hepatocyte apoptotic process / positive regulation of cytokinesis / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / mitotic cytokinesis / endocytic vesicle / vesicle-mediated transport / ruffle / MHC class II antigen presentation / cellular response to nerve growth factor stimulus / liver development / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / recycling endosome / mitotic spindle / spindle / recycling endosome membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / protein transport / presynapse / myelin sheath / cell cortex / early endosome membrane / midbody / microtubule binding / microtubule / early endosome / endosome / cell cycle / cell division / focal adhesion / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Makyio, H. / Takei, T. / Ohgi, H. / Takahashi, S. / Takatsu, H. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. ...Makyio, H. / Takei, T. / Ohgi, H. / Takahashi, S. / Takatsu, H. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. / Wakatsuki, S. / Nakayama, K. | ||||||
![]() | ![]() Title: Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis Authors: Makyio, H. / Ohgi, M. / Takei, T. / Takahashi, S. / Takatsu, H. / Katoh, Y. / Hanai, A. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. ...Authors: Makyio, H. / Ohgi, M. / Takei, T. / Takahashi, S. / Takatsu, H. / Katoh, Y. / Hanai, A. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. / Wakatsuki, S. / Nakayama, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 444.3 KB | Display | ![]() |
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PDB format | ![]() | 363.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 54 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j5xS 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
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 19990.898 Da / Num. of mol.: 4 / Fragment: UNP residues 13-175 / Mutation: Q67L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 13515.261 Da / Num. of mol.: 4 / Fragment: UNP residues 794-911 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 114 molecules ![](data/chem/img/GTP.gif)
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#3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 4000, 0.05M ammonium sulfate, 0.005M magnesium chloride, 0.1M sodium cacodylate, 0.25-1.0% v/v ethyl acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2010 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.809→87.286 Å / Num. all: 29002 / Num. obs: 28794 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.7 |
Reflection shell | Resolution: 2.8→2.85 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2J5X Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0 / SU B: 32.573 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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 max: 143.52 Å2 / Biso mean: 55.8034 Å2 / Biso min: 16.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.809→2.881 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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