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- EMDB-78112: 1-protofilament map of taxol stabilized human microtubule using C... -

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Basic information

Entry
Database: EMDB / ID: EMD-78112
Title1-protofilament map of taxol stabilized human microtubule using CsMT workflow
Map data
Sample
  • Organelle or cellular component: 13-protofilament microtubule
Keywordsmicrotubule / CsMT / CryoSPARC / single-particle analysis / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsAlagha T / Arin A / Parfitt HG / Legal T / Bui KH
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: CsMT: a robust and streamlined CryoSPARC workflow for cryo-EM reconstruction of microtubules.
Authors: Tina Alagha / Asuva Arin / Nicholas Vangos / Helena Goodey-Parfitt / Hai Nguyen Ngo / Nhat Nam Dau / Minh Hoa Nguyen / Thibault Legal / Michael A Cianfrocco / Khanh Huy Bui /
Abstract: Microtubules are cytoskeletal filaments that are involved in intracellular transport, cell division and motility. Despite their biological importance, determining their high-resolution structures via ...Microtubules are cytoskeletal filaments that are involved in intracellular transport, cell division and motility. Despite their biological importance, determining their high-resolution structures via cryo-electron microscopy remains a significant technical challenge due to their polymorphism and pseudo-helical assembly. Current processing workflows are complex, often requiring the integration of multiple software packages and custom scripts, which creates a steep learning curve for many research groups. To address these limitations, we introduce CsMT, a streamlined workflow implemented entirely within the CryoSPARC environment and using synthetic references. CsMT simplifies microtubule reconstruction by utilizing a novel protofilament-pair classification approach, which effectively handles the inherent pseudo-symmetry and structural heterogeneity of microtubules with minimal manual intervention. Our workflow is versatile, and is capable of processing both undecorated and decorated microtubules while accurately determining seams and performing high-resolution refinement. We demonstrate the efficacy of this workflow by achieving 2.3 and 2.7 Å resolution reconstructions of homotypic and heterotypic maps of undecorated microtubules, matching the best-resolved microtubule structures in the field. By unifying the pipeline into a single and portable workflow, CsMT enhances reproducibility and accessibility, empowering more laboratories to explore the structural biology of microtubules and associated proteins, yielding new insights into their function.
History
DepositionJul 16, 2026-
Header (metadata) releaseOct 21, 2026-
Map releaseOct 21, 2026-
UpdateOct 21, 2026-
Current statusOct 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78112.png

Downloads & links

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Map

FileDownload / File: emd_78112.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.29289523 - 0.5744387
Average (Standard dev.)0.00010982105 (±0.010398526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_78112_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_78112_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_78112_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : 13-protofilament microtubule

EntireName: 13-protofilament microtubule
Components
  • Organelle or cellular component: 13-protofilament microtubule

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Supramolecule #1: 13-protofilament microtubule

SupramoleculeName: 13-protofilament microtubule / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.2) / Number images used: 1275502
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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