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- PDB-6s8m: S. pombe microtubule decorated with Cut7 motor domain in the AMPP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6s8m | |||||||||
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Title | S. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state | |||||||||
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![]() | MOTOR PROTEIN / S. pombe / microtubule / kinesin-5 / Cut7 motor domain | |||||||||
Function / homology | ![]() mitotic spindle pole body duplication / Platelet degranulation / mitotic spindle formation (spindle phase one) / mitotic spindle elongation (spindle phase three) / Kinesins / initial mitotic spindle pole body separation / microtubule plus-end directed mitotic chromosome migration / nuclear migration by microtubule mediated pushing forces / meiotic spindle pole / meiotic spindle assembly ...mitotic spindle pole body duplication / Platelet degranulation / mitotic spindle formation (spindle phase one) / mitotic spindle elongation (spindle phase three) / Kinesins / initial mitotic spindle pole body separation / microtubule plus-end directed mitotic chromosome migration / nuclear migration by microtubule mediated pushing forces / meiotic spindle pole / meiotic spindle assembly / nuclear division / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle pole body / mitotic spindle midzone / astral microtubule / spindle elongation / polar microtubule / minus-end-directed microtubule motor activity / plus-end-directed microtubule motor activity / meiotic spindle / microtubule associated complex / microtubule motor activity / intracellular distribution of mitochondria / cytoplasmic microtubule / mitotic spindle assembly / cytoplasmic microtubule organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / structural constituent of cytoskeleton / mitotic spindle / kinetochore / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / response to antibiotic / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Moores, C.A. / von Loeffelholz, O. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structure (4.5-Å) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance. Authors: Ottilie von Loeffelholz / Alejandro Peña / Douglas Robert Drummond / Robert Cross / Carolyn Ann Moores / ![]() Abstract: Kinesin-5s are microtubule-dependent motors that drive spindle pole separation during mitosis. We used cryo-electron microscopy to determine the 4.5-Å resolution structure of the motor domain of the ...Kinesin-5s are microtubule-dependent motors that drive spindle pole separation during mitosis. We used cryo-electron microscopy to determine the 4.5-Å resolution structure of the motor domain of the fission yeast kinesin-5 Cut7 bound to fission yeast microtubules and explored the topology of the motor-microtubule interface and the susceptibility of the complex to drug binding. Despite their non-canonical architecture and mechanochemistry, Schizosaccharomyces pombe microtubules were stabilized by epothilone at the taxane binding pocket. The overall Cut7 footprint on the S. pombe microtubule surface is altered compared to mammalian tubulin microtubules because of their different polymer architectures. However, the core motor-microtubule interaction is tightly conserved, reflected in similar Cut7 ATPase activities on each microtubule type. AMPPNP-bound Cut7 adopts a kinesin-conserved ATP-like conformation including cover neck bundle formation. However, the Cut7 ATPase is not blocked by a mammalian-specific kinesin-5 inhibitor, consistent with the non-conserved sequence and structure of its loop5 insertion. #1: Journal: J Mol Biol / Year: 2020 Title: Corrigendum to "Cryo-EM Structure (4.5 Å) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance" [J. Mol. Biol. 431 (2019) 864-872] ...Title: Corrigendum to "Cryo-EM Structure (4.5 Å) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance" [J. Mol. Biol. 431 (2019) 864-872] https://doi.org/10.1016/j.jmb.2019.01.011. Authors: Ottilie von Loeffelholz / Alejandro Peña / Douglas Robert Drummond / Robert Cross / Carolyn Ann Moores / ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.5 KB | Display | ![]() |
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PDB format | ![]() | 177.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 38.1 KB | Display | |
Data in CIF | ![]() | 57.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3527MC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules KBA
#1: Protein | Mass: 48219.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cut7, SPAC25G10.07c / Production host: ![]() ![]() |
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#2: Protein | Mass: 49518.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nda3, alp12, SPBC26H8.07c / Production host: ![]() ![]() |
#3: Protein | Mass: 51203.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nda2, SPBC16A3.15c / Production host: ![]() ![]() |
-Non-polymers , 5 types, 5 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/EPB.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/EPB.gif)
![](data/chem/img/GTP.gif)
#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-ANP / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-EPB / |
#8: Chemical | ChemComp-GTP / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Microtubule decorated with Cut7 motor domain and stabilized by epothilone-B Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.3 mm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Details: inside Frealign reconstruction procedure / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33007 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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