[English] 日本語
Yorodumi- EMDB-3529: Ustilago maydis kinesin-5 motor domain in the AMPPNP state bound ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3529 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ustilago maydis kinesin-5 motor domain in the AMPPNP state bound to microtubules | |||||||||
Map data | microtubule decorated with Ustillago maydis kinesin-5 motor domain in the AMPPNP state | |||||||||
Sample |
| |||||||||
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 / structural constituent of cytoskeleton / mitotic spindle / 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 / structural constituent of cytoskeleton / mitotic spindle / 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 (strain 521 / FGSC 9021) (fungus) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Moores CA / von Loeffelholz O | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3529.map.gz | 1.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3529-v30.xml emd-3529.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
Images | emd_3529.png | 220.8 KB | ||
Filedesc metadata | emd-3529.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3529 | HTTPS FTP |
-Validation report
Summary document | emd_3529_validation.pdf.gz | 256.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3529_full_validation.pdf.gz | 255.5 KB | Display | |
Data in XML | emd_3529_validation.xml.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3529 | HTTPS FTP |
-Related structure data
Related structure data | 5mm4MC 3530C 5mm7C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_3529.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | microtubule decorated with Ustillago maydis kinesin-5 motor domain in the AMPPNP state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-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: Ustilago maydis kinesin-5
+Supramolecule #3: alpha-beta-tubulin
+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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
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: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Details: 13x symmetrisation / Number images used: 13581 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |