[English] 日本語
Yorodumi- EMDB-6750: Representative tomogram for the Trypanosoma brucei zoid cell with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6750 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Representative tomogram for the Trypanosoma brucei zoid cell without flagellar wave | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Trypanosoma brucei (eukaryote) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Sun SY / Kaelber JT / Chen M / Shi J / Schmid MF / Chiu W / He CY | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Flagellum couples cell shape to motility in . Authors: Stella Y Sun / Jason T Kaelber / Muyuan Chen / Xiaoduo Dong / Yasaman Nematbakhsh / Jian Shi / Matthew Dougherty / Chwee Teck Lim / Michael F Schmid / Wah Chiu / Cynthia Y He / Abstract: In the unicellular parasite the causative agent of human African sleeping sickness, complex swimming behavior is driven by a flagellum laterally attached to the long and slender cell body. Using ...In the unicellular parasite the causative agent of human African sleeping sickness, complex swimming behavior is driven by a flagellum laterally attached to the long and slender cell body. Using microfluidic assays, we demonstrated that can penetrate through an orifice smaller than its maximum diameter. Efficient motility and penetration depend on active flagellar beating. To understand how active beating of the flagellum affects the cell body, we genetically engineered to produce anucleate cytoplasts (zoids and minis) with different flagellar attachment configurations and different swimming behaviors. We used cryo-electron tomography (cryo-ET) to visualize zoids and minis vitrified in different motility states. We showed that flagellar wave patterns reflective of their motility states are coupled to cytoskeleton deformation. Based on these observations, we propose a mechanism for how flagellum beating can deform the cell body via a flexible connection between the flagellar axoneme and the cell body. This mechanism may be critical for to disseminate in its host through size-limiting barriers. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6750.map.gz | 554.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6750-v30.xml emd-6750.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_6750.png | 71.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6750 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6750 | HTTPS FTP |
-Validation report
Summary document | emd_6750_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6750_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_6750_validation.xml.gz | 499 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6750 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6750 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6750.map.gz / Format: CCP4 / Size: 733.1 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 57.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Trypanosoma brucei cell
Entire | Name: Trypanosoma brucei cell |
---|---|
Components |
|
-Supramolecule #1: Trypanosoma brucei cell
Supramolecule | Name: Trypanosoma brucei cell / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Trypanosoma brucei (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.2 |
---|---|
Grid | Model: EMS lacey carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | 2,000-3,000 cells/ml |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Electron Microsocpy Science / Diameter: 25 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 40 |
---|