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Yorodumi- PDB-6vpo: Cryo-EM structure of microtubule-bound KLP61F motor domain in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vpo | |||||||||
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Title | Cryo-EM structure of microtubule-bound KLP61F motor domain in the AMPPNP state | |||||||||
Components |
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Keywords | MOTOR PROTEIN / Kinesin-5 / microtubules / mitotic spindles / AMPPNP state / cell cycle | |||||||||
Function / homology | Function and homology information aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / microtubule bundle formation ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / microtubule bundle formation / positive regulation of Golgi to plasma membrane protein transport / plus-end-directed microtubule motor activity / mitotic centrosome separation / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / protein secretion / mitotic spindle assembly / mitotic spindle organization / spindle microtubule / mitotic spindle / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Bodrug, T. / Wilson-Kubalek, E.M. / Nithianantham, S. / Debs, G. / Sindelar, C.V. / Milligan, R. / Al-Bassam, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2020 Title: The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding. Authors: Tatyana Bodrug / Elizabeth M Wilson-Kubalek / Stanley Nithianantham / Alex F Thompson / April Alfieri / Ignas Gaska / Jennifer Major / Garrett Debs / Sayaka Inagaki / Pedro Gutierrez / ...Authors: Tatyana Bodrug / Elizabeth M Wilson-Kubalek / Stanley Nithianantham / Alex F Thompson / April Alfieri / Ignas Gaska / Jennifer Major / Garrett Debs / Sayaka Inagaki / Pedro Gutierrez / Larisa Gheber / Richard J McKenney / Charles Vaughn Sindelar / Ronald Milligan / Jason Stumpff / Steven S Rosenfeld / Scott T Forth / Jawdat Al-Bassam / Abstract: Kinesin-5 motors organize mitotic spindles by sliding apart microtubules. They are homotetramers with dimeric motor and tail domains at both ends of a bipolar minifilament. Here, we describe a ...Kinesin-5 motors organize mitotic spindles by sliding apart microtubules. They are homotetramers with dimeric motor and tail domains at both ends of a bipolar minifilament. Here, we describe a regulatory mechanism involving direct binding between tail and motor domains and its fundamental role in microtubule sliding. Kinesin-5 tails decrease microtubule-stimulated ATP-hydrolysis by specifically engaging motor domains in the nucleotide-free or ADP states. Cryo-EM reveals that tail binding stabilizes an open motor domain ATP-active site. Full-length motors undergo slow motility and cluster together along microtubules, while tail-deleted motors exhibit rapid motility without clustering. The tail is critical for motors to zipper together two microtubules by generating substantial sliding forces. The tail is essential for mitotic spindle localization, which becomes severely reduced in tail-deleted motors. Our studies suggest a revised microtubule-sliding model, in which kinesin-5 tails stabilize motor domains in the microtubule-bound state by slowing ATP-binding, resulting in high-force production at both homotetramer ends. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vpo.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vpo.ent.gz | 173 KB | Display | PDB format |
PDBx/mmJSON format | 6vpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vpo_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6vpo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6vpo_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 6vpo_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/6vpo ftp://data.pdbj.org/pub/pdb/validation_reports/vp/6vpo | HTTPS FTP |
-Related structure data
Related structure data | 21314MC 6vppC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550 |
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 |
#3: Protein | Mass: 42627.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Klp61F, KLP2, CG9191 / Production host: Escherichia coli (E. coli) / References: UniProt: P46863 |
-Non-polymers , 4 types, 4 molecules
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-ANP / |
-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: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -34.61 ° / Axial rise/subunit: 17.4 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 73451 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39220 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | B value: 216 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient |