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- EMDB-72661: CryoEM map of microtubules generated from tubulin partitioned int... -

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Basic information

Entry
Database: EMDB / ID: EMD-72661
TitleCryoEM map of microtubules generated from tubulin partitioned into droplets of delta351-1438 CLIP-170
Map data
Sample
  • Complex: Microtubules generated from HiLyte 488-labelled tubulin.
KeywordsMicrotubule / PROTEIN FIBRIL
Biological speciesSus scrofa domesticus (domestic pig)
Methodhelical reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsLi Q / Boyko S / Surewicz K / Surewicz WK
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Biol Chem / Year: 2025
Title: Distinct liquid-liquid phase separation properties of end-binding proteins EB1 and EB3.
Authors: Solomiia Boyko / Qiuye Li / Krystyna Surewicz / Witold K Surewicz /
Abstract: End-binding proteins (EBs) are central components of the network of microtubule-plus-end-tracking proteins (+TIPs) that modulate microtubule dynamics. Recent studies have shown that EBs undergo ...End-binding proteins (EBs) are central components of the network of microtubule-plus-end-tracking proteins (+TIPs) that modulate microtubule dynamics. Recent studies have shown that EBs undergo liquid-liquid phase separation (LLPS), and it was proposed that the resulting condensates could play a major role in the recruitment of other + TIPs as well as in polymerization of tubulin. Here, we performed detailed studies of LLPS properties of two major members of the EB family in mammalian cells, EB1 and EB3. Surprisingly, we found that, despite 67% sequence identity, EB3 has a significantly higher LLPS propensity than EB1, both in vitro and in cells. This difference is due to combined contributions from multiple protein regions, with histidine residues in the N-terminal domain playing a particularly important role. Furthermore, EB1 and EB3 condensates were found to differ in their material properties, with EB3 droplets being much less dynamic than the EB1 counterparts. Importantly, EB3 droplets had higher capacity to recruit tubulin and nucleate its polymerization. The differences with regard to the impact of condensation on tubulin polymerization were especially striking in the presence of another + TIP-associated protein, CLIP-170, in which case higher tubulin polymerization capacity was observed for EB3/CLIP-170 droplets than the EB1/CLIP-170 counterparts, and this difference was attributed to distinct material properties of the two droplet types. These findings suggest that different, EB-dependent + TIP body types may exist in cells, contributing to functional specialization of microtubules.
History
DepositionSep 10, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72661.png

Downloads & links

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Map

FileDownload / File: emd_72661.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 423.936 Å		0.83 Å/pix.
x 512 pix.
= 423.936 Å		0.83 Å/pix.
x 512 pix.
= 423.936 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.009304137 - 0.014843882
Average (Standard dev.)0.00011678608 (±0.00090964796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 423.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72661_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72661_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72661_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Microtubules generated from HiLyte 488-labelled tubulin.

EntireName: Microtubules generated from HiLyte 488-labelled tubulin.
Components
  • Complex: Microtubules generated from HiLyte 488-labelled tubulin.

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Supramolecule #1: Microtubules generated from HiLyte 488-labelled tubulin.

SupramoleculeName: Microtubules generated from HiLyte 488-labelled tubulin.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa domesticus (domestic pig)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -128.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 9921
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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