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- PDB-5mm7: Ustilago maydis kinesin-5 motor domain with N-terminal extension ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mm7 | ||||||
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Title | Ustilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state bound to microtubules | ||||||
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![]() | MOTOR PROTEIN / Ustilago maydis / kinesin-5 | ||||||
Function / homology | ![]() initial mitotic spindle pole body separation / spindle elongation / minus-end-directed microtubule motor activity / plus-end-directed microtubule motor activity / microtubule-based movement / mitotic spindle assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / structural constituent of cytoskeleton / mitotic spindle ...initial mitotic spindle pole body separation / spindle elongation / minus-end-directed microtubule motor activity / plus-end-directed microtubule motor activity / microtubule-based movement / mitotic spindle assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / 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 | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||
![]() | Moores, C.A. / von Loeffelholz, O. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.2 KB | Display | ![]() |
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PDB format | ![]() | 183.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 58.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3530MC ![]() 3529C ![]() 5mm4C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules KAB
#1: Protein | Mass: 49482.207 Da / Num. of mol.: 1 / Fragment: motor domain, UNP residues 1-456 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 48769.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 47940.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 6 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/GDP.gif)
#4: Chemical | #5: Chemical | ChemComp-ANP / | #6: Chemical | ChemComp-GTP / | #7: Chemical | ChemComp-TA1 / | #8: Chemical | ChemComp-GDP / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||||||||||||
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 |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12629 / Details: 13x symmetrisation / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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