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- EMDB-14108: Microtubule plus-end in presence of Mal3 -

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Basic information

Entry
Database: EMDB / ID: EMD-14108
TitleMicrotubule plus-end in presence of Mal3
Map dataGrowing microtubule minus-end in presence of Mal3
Sample
  • Organelle or cellular component: Growing microtubule minus-end in presence of Tip1, Tea2 and Mal3
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodelectron tomography / cryo EM
AuthorsVolkov VA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)609822European Union
CitationJournal: Nat Cell Biol / Year: 2023
Title: Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus-ends.
Authors: Renu Maan / Louis Reese / Vladimir A Volkov / Matthew R King / Eli O van der Sluis / Nemo Andrea / Wiel H Evers / Arjen J Jakobi / Marileen Dogterom /
Abstract: Growing microtubule ends organize end-tracking proteins into comets of mixed composition. Here using a reconstituted fission yeast system consisting of end-binding protein Mal3, kinesin Tea2 and ...Growing microtubule ends organize end-tracking proteins into comets of mixed composition. Here using a reconstituted fission yeast system consisting of end-binding protein Mal3, kinesin Tea2 and cargo Tip1, we found that these proteins can be driven into liquid-phase droplets both in solution and at microtubule ends under crowding conditions. In the absence of crowding agents, cryo-electron tomography revealed that motor-dependent comets consist of disordered networks where multivalent interactions may facilitate non-stoichiometric accumulation of cargo Tip1. We found that two disordered protein regions in Mal3 are required for the formation of droplets and motor-dependent accumulation of Tip1, while autonomous Mal3 comet formation requires only one of them. Using theoretical modelling, we explore possible mechanisms by which motor activity and multivalent interactions may lead to the observed enrichment of Tip1 at microtubule ends. We conclude that microtubule ends may act as platforms where multivalent interactions condense microtubule-associated proteins into large multi-protein complexes.
History
DepositionJan 3, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateMar 8, 2023-
Current statusMar 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14108.png

Downloads & links

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Map

FileDownload / File: emd_14108.map.gz / Format: CCP4 / Size: 3.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGrowing microtubule minus-end in presence of Mal3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.34 Å/pix.
x 260 pix.
= 1908.4 Å		7.34 Å/pix.
x 1920 pix.
= 14092.801 Å		7.34 Å/pix.
x 1856 pix.
= 13623.04 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.34 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-715.98865 - 816.8375
Average (Standard dev.)2.1135979 (±42.209473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-3231-130
Dimensions19201856260
Spacing18561920260
CellA: 13623.04 Å / B: 14092.801 Å / C: 1908.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Growing microtubule minus-end in presence of Tip1, Tea2 and Mal3

EntireName: Growing microtubule minus-end in presence of Tip1, Tea2 and Mal3
Components
  • Organelle or cellular component: Growing microtubule minus-end in presence of Tip1, Tea2 and Mal3

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Supramolecule #1: Growing microtubule minus-end in presence of Tip1, Tea2 and Mal3

SupramoleculeName: Growing microtubule minus-end in presence of Tip1, Tea2 and Mal3
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 6.9
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma / Diameter: 5 nm

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus min: 4.0 µm / Nominal magnification: 10000

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Image processing

Final reconstructionNumber images used: 61

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