+Open data
-Basic information
Entry | Database: PDB / ID: 3lre | ||||||
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Title | Crystal Structure Analysis of Human Kinesin-8 Motor Domain | ||||||
Components | Kinesin-like protein KIF18A | ||||||
Keywords | MOTOR PROTEIN / nucleotide binding / microtubule binding / ATP-binding / Cell projection / Cytoskeleton / Glycoprotein / Microtubule / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / Transport | ||||||
Function / homology | Function and homology information tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization ...tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization / kinesin complex / mitotic metaphase chromosome alignment / microtubule-based movement / seminiferous tubule development / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of microtubule cytoskeleton organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / ruffle / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / cellular response to estradiol stimulus / caveola / RHO GTPases Activate Formins / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / protein transport / actin binding / microtubule binding / centrosome / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Brejc, K. / Moores, C.A. / Hartman, J. | ||||||
Citation | Journal: EMBO J / Year: 2010 Title: Insight into the molecular mechanism of the multitasking kinesin-8 motor. Authors: Carsten Peters / Katjuša Brejc / Lisa Belmont / Andrew J Bodey / Yan Lee / Ming Yu / Jun Guo / Roman Sakowicz / James Hartman / Carolyn A Moores / Abstract: Members of the kinesin-8 motor class have the remarkable ability to both walk towards microtubule plus-ends and depolymerise these ends on arrival, thereby regulating microtubule length. To analyse ...Members of the kinesin-8 motor class have the remarkable ability to both walk towards microtubule plus-ends and depolymerise these ends on arrival, thereby regulating microtubule length. To analyse how kinesin-8 multitasks, we studied the structure and function of the kinesin-8 motor domain. We determined the first crystal structure of a kinesin-8 and used cryo-electron microscopy to calculate the structure of the microtubule-bound motor. Microtubule-bound kinesin-8 reveals a new conformation compared with the crystal structure, including a bent conformation of the α4 relay helix and ordering of functionally important loops. The kinesin-8 motor domain does not depolymerise stabilised microtubules with ATP but does form tubulin rings in the presence of a non-hydrolysable ATP analogue. This shows that, by collaborating, kinesin-8 motor domain molecules can release tubulin from microtubules, and that they have a similar mechanical effect on microtubule ends as kinesin-13, which enables depolymerisation. Our data reveal aspects of the molecular mechanism of kinesin-8 motors that contribute to their unique dual motile and depolymerising functions, which are adapted to control microtubule length. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lre.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lre.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/3lre ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lre | HTTPS FTP |
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-Related structure data
Related structure data | 1701C 1702C 1t5cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39788.254 Da / Num. of mol.: 2 / Fragment: UNP residues 1-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF18A, OK/SW-cl.108 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8NI77 #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: 2.44 Å3/Da / Density % sol: 49.53 % |
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Crystal grow | Temperature: 275 K / Method: vapor diffusion / pH: 7.8 Details: 10-13% PEG 20000, 0.1M HEPES pH 7.8, 2% dioxane, vapor diffusion, temperature 275K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: BRUKER AXS PROTEUM/R6000 / Detector: CCD / Date: Apr 12, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→70.71 Å / Num. obs: 39803 / % possible obs: 98.8 % / Rsym value: 0.064 / Net I/σ(I): 6.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T5C Resolution: 2.2→70.71 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.301 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.753 / SU B: 5.875 / SU ML: 0.151 / SU R Cruickshank DPI: 0.269 / SU Rfree: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.66 Å2 / Biso mean: 33.274 Å2 / Biso min: 10.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→70.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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