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- EMDB-15536: Plasmodium falciparum gametocyte subpellicular microtubule with 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-15536
TitlePlasmodium falciparum gametocyte subpellicular microtubule with 15 protofilaments determined in situ
Map dataIn situ subtomogram average of Plasmodium falciparum subpellicular microtubule with 15 protofilaments
Sample
  • Cell: Plasmodium falciparum gametocyte
KeywordsCytoskeleton / microtubules / STRUCTURAL PROTEIN
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsFerreira JL / Prazak V / Vasishtan D / Grunewald K / Siggel M / Hentzschel F / Pietsch E / Kosinski J / Frischknecht F / Gilberger TW
Funding support France, United Kingdom, Germany, 3 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000024/2020-L France
Wellcome Trust107806/Z/15/Z and 209250/Z/17/ Z United Kingdom
German Research Foundation (DFG)SFB 1129, SPP 2332, SPP 2225 and grant FR 2140/10-1 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Variable microtubule architecture in the malaria parasite.
Authors: Josie L Ferreira / Vojtěch Pražák / Daven Vasishtan / Marc Siggel / Franziska Hentzschel / Annika M Binder / Emma Pietsch / Jan Kosinski / Friedrich Frischknecht / Tim W Gilberger / Kay Grünewald /
Abstract: Microtubules are a ubiquitous eukaryotic cytoskeletal element typically consisting of 13 protofilaments arranged in a hollow cylinder. This arrangement is considered the canonical form and is adopted ...Microtubules are a ubiquitous eukaryotic cytoskeletal element typically consisting of 13 protofilaments arranged in a hollow cylinder. This arrangement is considered the canonical form and is adopted by most organisms, with rare exceptions. Here, we use in situ electron cryo-tomography and subvolume averaging to analyse the changing microtubule cytoskeleton of Plasmodium falciparum, the causative agent of malaria, throughout its life cycle. Unexpectedly, different parasite forms have distinct microtubule structures coordinated by unique organising centres. In merozoites, the most widely studied form, we observe canonical microtubules. In migrating mosquito forms, the 13 protofilament structure is further reinforced by interrupted luminal helices. Surprisingly, gametocytes contain a wide distribution of microtubule structures ranging from 13 to 18 protofilaments, doublets and triplets. Such a diversity of microtubule structures has not been observed in any other organism to date and is likely evidence of a distinct role in each life cycle form. This data provides a unique view into an unusual microtubule cytoskeleton of a relevant human pathogen.
History
DepositionAug 5, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15536.png

Downloads & links

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Map

FileDownload / File: emd_15536.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ subtomogram average of Plasmodium falciparum subpellicular microtubule with 15 protofilaments
Voxel sizeX=Y=Z: 6.672 Å
Density
Contour LevelBy AUTHOR: 0.897
Minimum - Maximum-3.006786 - 5.4545307
Average (Standard dev.)-0.000000000057716 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 533.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Unsharpened half map 2

Fileemd_15536_half_map_1.map
AnnotationUnsharpened half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map 1

Fileemd_15536_half_map_2.map
AnnotationUnsharpened half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 microtubules
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 / Details: RPMI
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsFIB-milled Plasmodium falciparum gametocytes

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 26000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 7 / Number images used: 10435
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Helical parameters - Δz: 10.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 24 °
Applied symmetry - Helical parameters - Axial symmetry: C15 (15 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 10345
FSC plot (resolution estimation)

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