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Yorodumi- EMDB-15538: Plasmodium falciparum gametocyte subpellicular microtubule with 1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15538 | ||||||||||||
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Title | Plasmodium falciparum gametocyte subpellicular microtubule with 17 protofilaments determined in situ | ||||||||||||
Map data | Plasmodium falciparum gametocyte subpellicular microtubule with 17 protofilaments determined in situ | ||||||||||||
Sample |
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Keywords | Cytoskeleton / microtubules / STRUCTURAL PROTEIN | ||||||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 20.0 Å | ||||||||||||
Authors | Ferreira 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
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15538.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-15538-v30.xml emd-15538.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15538_fsc.xml | 3.8 KB | Display | FSC data file |
Images | emd_15538.png | 105.1 KB | ||
Filedesc metadata | emd-15538.cif.gz | 4.4 KB | ||
Others | emd_15538_half_map_1.map.gz emd_15538_half_map_2.map.gz | 1.8 MB 1.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15538 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15538 | HTTPS FTP |
-Validation report
Summary document | emd_15538_validation.pdf.gz | 738.1 KB | Display | EMDB validaton report |
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Full document | emd_15538_full_validation.pdf.gz | 737.7 KB | Display | |
Data in XML | emd_15538_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | emd_15538_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15538 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15538 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15538.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Plasmodium falciparum gametocyte subpellicular microtubule with 17 protofilaments determined in situ | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.712 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Unsharpened half map 1
File | emd_15538_half_map_1.map | ||||||||||||
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Annotation | Unsharpened half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unsharpened half map 2
File | emd_15538_half_map_2.map | ||||||||||||
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Annotation | Unsharpened half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Plasmodium falciparum gametocyte
Entire | Name: Plasmodium falciparum gametocyte |
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Components |
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-Supramolecule #1: Plasmodium falciparum gametocyte
Supramolecule | Name: Plasmodium falciparum gametocyte / type: cell / ID: 1 / Parent: 0 / Details: Subpellicular microtubules |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Details: RPMI |
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Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
Details | FIB-milled Plasmodium falciparum gametocytes |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 26000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |