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- EMDB-56294: Plasmodium falciparum gametocyte microtubule with 15 protofilamen... -

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Basic information

Entry
Database: EMDB / ID: EMD-56294
TitlePlasmodium falciparum gametocyte microtubule with 15 protofilaments determined in situ
Map data
Sample
  • Cell: Plasmodium falciparum gametocyte
KeywordsCytoskeleton / Microtubule / STRUCTURAL PROTEIN
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsFerreira JL
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust227774/Z/23/Z United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Adaptations in Plasmodium tubulin determine distinct microtubule architectures, mechanics and drug susceptibility.
Authors: Mamata Bangera / Jiangbo Wu / Daniel Beckett / Dominik Fachet / Josie L Ferreira / Gregory A Voth / Simone Reber / Carolyn A Moores /
Abstract: Microtubules are ubiquitous yet diverse cytoskeleton filaments. However, tubulin conservation presents challenges in understanding the origins of diverse microtubule architectures. The mechanisms by ...Microtubules are ubiquitous yet diverse cytoskeleton filaments. However, tubulin conservation presents challenges in understanding the origins of diverse microtubule architectures. The mechanisms by which microtubule architecture varies through the life cycle of the malaria-causing parasite Plasmodium are not understood and provide a valuable framework for exploring how intrinsic properties of tubulin contribute to architectural variety. Using parasite-purified tubulin, we determine P. falciparum microtubule structures by cryo-electron microscopy. Parasite-specific sequences change the tubulin dimer structure, suggesting how drug susceptibility and polymer properties are modified. Within the P. falciparum microtubule, lateral contacts are smaller but stronger, and the lattice is stiffer than in brain microtubules. Non-canonical microtubule architectures found in parasites are highly similar to those observed in vitro, validating the physiological relevance of these properties. Our findings show how evolutionary adaptation of tubulin modulates the material properties of the microtubule cytoskeleton.
History
DepositionJan 11, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56294.png

Downloads & links

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Map

FileDownload / File: emd_56294.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
6.71 Å/pix.
x 80 pix.
= 536.96 Å		6.71 Å/pix.
x 80 pix.
= 536.96 Å		6.71 Å/pix.
x 80 pix.
= 536.96 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 6.712 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.86
Minimum - Maximum-17.605702999999998 - 24.588850000000001
Average (Standard dev.)-0.051029798 (±3.8446596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin353535
Dimensions808080
Spacing808080
CellA=B=C: 536.95996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56294_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_56294_half_map_2.map
Projections & Slices
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Sample components

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Entire : Plasmodium falciparum gametocyte

EntireName: Plasmodium falciparum gametocyte
Components
  • Cell: Plasmodium falciparum gametocyte

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Supramolecule #1: Plasmodium falciparum gametocyte

SupramoleculeName: Plasmodium falciparum gametocyte / type: cell / ID: 1 / Parent: 0
Details: Subpellicular and nuclear microtubules with 15 protofilaments
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: RPMI
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER / Details: Manually plunged in humidity controlled room.
DetailsLawn of cells - FIB-milled

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 26000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 12422
ExtractionNumber tomograms: 10 / Number images used: 4000 / Software - Name: PEET
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model

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