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Yorodumi- EMDB-10422: Human kinesin-5 motor domain in the AMPPNP state bound to microtubules -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10422 | |||||||||||||||
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Title | Human kinesin-5 motor domain in the AMPPNP state bound to microtubules | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | kinesin / microtubule / mitosis / inhibition / motor / CELL CYCLE | |||||||||||||||
Function / homology | Function and homology information spindle elongation / regulation of mitotic centrosome separation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III ...spindle elongation / regulation of mitotic centrosome separation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / mitotic centrosome separation / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / spindle pole / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / cell division / GTPase activity / GTP binding / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||||||||
Authors | Pena AP / Sweeney A | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Structure / Year: 2020 Title: Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy. Authors: Alejandro Peña / Aaron Sweeney / Alexander D Cook / Julia Locke / Maya Topf / Carolyn A Moores / Abstract: Kinesin-5 motors are vital mitotic spindle components, and disruption of their function perturbs cell division. We investigated the molecular mechanism of the human kinesin-5 inhibitor GSK-1, which ...Kinesin-5 motors are vital mitotic spindle components, and disruption of their function perturbs cell division. We investigated the molecular mechanism of the human kinesin-5 inhibitor GSK-1, which allosterically promotes tight microtubule binding. GSK-1 inhibits monomeric human kinesin-5 ATPase and microtubule gliding activities, and promotes the motor's microtubule stabilization activity. Using cryoelectron microscopy, we determined the 3D structure of the microtubule-bound motor-GSK-1 at 3.8 Å overall resolution. The structure reveals that GSK-1 stabilizes the microtubule binding surface of the motor in an ATP-like conformation, while destabilizing regions of the motor around the empty nucleotide binding pocket. Density corresponding to GSK-1 is located between helix-α4 and helix-α6 in the motor domain at its interface with the microtubule. Using a combination of difference mapping and protein-ligand docking, we characterized the kinesin-5-GSK-1 interaction and further validated this binding site using mutagenesis. This work opens up new avenues of investigation of kinesin inhibition and spindle perturbation. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10422.map.gz | 460.2 KB | EMDB map data format | |
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Header (meta data) | emd-10422-v30.xml emd-10422.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10422_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_10422.png | 159.8 KB | ||
Filedesc metadata | emd-10422.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10422 | HTTPS FTP |
-Validation report
Summary document | emd_10422_validation.pdf.gz | 429.7 KB | Display | EMDB validaton report |
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Full document | emd_10422_full_validation.pdf.gz | 429.3 KB | Display | |
Data in XML | emd_10422_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_10422_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10422 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10422 | HTTPS FTP |
-Related structure data
Related structure data | 6ta4MC 6ta3C 6tiwC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10422.map.gz / Format: CCP4 / Size: 2.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : AMPPNP bound Human Eg5 motor domain in complex with alpha/beta tubulin
+Supramolecule #1: AMPPNP bound Human Eg5 motor domain in complex with alpha/beta tubulin
+Supramolecule #2: AMPPNP bound Human Eg5 motor domain in complex with alpha/beta tubulin
+Supramolecule #3: AMPPNP bound Human Eg5 motor domain in complex with alpha/beta tubulin
+Macromolecule #1: Tubulin beta chain
+Macromolecule #2: Tubulin alpha-1B chain
+Macromolecule #3: Kinesin-like protein KIF11
+Macromolecule #4: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #7: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |