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Yorodumi- EMDB-3530: Ustilago maydis kinesin-5 motor domain with N-terminal extension ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3530 | |||||||||
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Title | Ustilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state bound to microtubules | |||||||||
Map data | Microtubule-bound Ustilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state | |||||||||
Sample |
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Keywords | Ustilago maydis / kinesin-5 / motor protein | |||||||||
Function / homology | Function and homology information initial mitotic spindle pole body separation / spindle elongation / plus-end-directed microtubule motor activity / microtubule-based movement / mitotic spindle assembly / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic spindle / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...initial mitotic spindle pole body separation / spindle elongation / plus-end-directed microtubule motor activity / microtubule-based movement / mitotic spindle assembly / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic spindle / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / GTPase activity / GTP binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Ustilago maydis (fungus) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | |||||||||
Authors | Moores CA / von Loeffelholz O | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: J Struct Biol / Year: 2019 Title: Cryo-EM structure of the Ustilago maydis kinesin-5 motor domain bound to microtubules. Authors: Ottilie von Loeffelholz / Carolyn Ann Moores / Abstract: In many eukaryotes, kinesin-5 motors are essential for mitosis, and small molecules that inhibit human kinesin-5 disrupt cell division. To investigate whether fungal kinesin-5s could be targets for ...In many eukaryotes, kinesin-5 motors are essential for mitosis, and small molecules that inhibit human kinesin-5 disrupt cell division. To investigate whether fungal kinesin-5s could be targets for novel fungicides, we studied kinesin-5 from the pathogenic fungus Ustilago maydis. We used cryo-electron microscopy to determine the microtubule-bound structure of its motor domain with and without the N-terminal extension. The ATP-like conformations of the motor in the presence or absence of this N-terminus are very similar, suggesting this region is structurally disordered and does not directly influence the motor ATPase. The Ustilago maydis kinesin-5 motor domain adopts a canonical ATP-like conformation, thereby allowing the neck linker to bind along the motor domain towards the microtubule plus end. However, several insertions within this motor domain are structurally distinct. Loop2 forms a non-canonical interaction with α-tubulin, while loop8 may bridge between two adjacent protofilaments. Furthermore, loop5 - which in human kinesin-5 is involved in binding allosteric inhibitors - protrudes above the nucleotide binding site, revealing a distinct binding pocket for potential inhibitors. This work highlights fungal-specific elaborations of the kinesin-5 motor domain and provides the structural basis for future investigations of kinesins as targets for novel fungicides. | |||||||||
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_3530.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-3530-v30.xml emd-3530.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
Images | emd_3530.png | 184.9 KB | ||
Filedesc metadata | emd-3530.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3530 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3530 | HTTPS FTP |
-Validation report
Summary document | emd_3530_validation.pdf.gz | 243.7 KB | Display | EMDB validaton report |
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Full document | emd_3530_full_validation.pdf.gz | 242.8 KB | Display | |
Data in XML | emd_3530_validation.xml.gz | 4.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3530 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3530 | HTTPS FTP |
-Related structure data
Related structure data | 5mm7MC 3529C 5mm4C 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_3530.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Microtubule-bound Ustilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Ternary complex of alpha-beta-tubulin stabilized by taxol and dec...
+Supramolecule #1: Ternary complex of alpha-beta-tubulin stabilized by taxol and dec...
+Supramolecule #2: kinesin-5
+Supramolecule #3: Tubulin alpha-1A chain
+Supramolecule #4: Tubulin beta chain
+Macromolecule #1: kinesin-5
+Macromolecule #2: Tubulin alpha-1A chain
+Macromolecule #3: Tubulin beta chain
+Macromolecule #4: MAGNESIUM ION
+Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #7: TAXOL
+Macromolecule #8: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.8 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Details: 13x symmetrisation / Number images used: 12629 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |