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- EMDB-6748: Representative tomogram for the Trypanosoma brucei mini cell -

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Basic information

Entry
Database: EMDB / ID: EMD-6748
TitleRepresentative tomogram for the Trypanosoma brucei mini cell
Map data
Sample
  • Cell: Trypanosoma brucei cell
Biological speciesTrypanosoma brucei (eukaryote)
Methodelectron tomography / cryo EM
AuthorsSun SY / Kaelber JT / Chen M / Shi J / Schmid MF / Chiu W / He CY
CitationJournal: 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
DepositionJun 10, 2017-
Header (metadata) releaseJun 13, 2018-
Map releaseJun 13, 2018-
UpdateDec 26, 2018-
Current statusDec 26, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_6748.png

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Map

FileDownload / File: emd_6748.map.gz / Format: CCP4 / Size: 511.7 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 42.54 Å
Density
Minimum - Maximum-128. - 127.
Average (Standard dev.)25.664850000000001 (±6.1620007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-11279
Dimensions19511528180
Spacing15281951180
CellA: 65001.12 Å / B: 82995.54 Å / C: 7657.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z42.5400006544542.53999948744242.54
M x/y/z15281951180
origin x/y/z0.0000.0000.000
length x/y/z65001.12182995.5397657.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-112-5679
NC/NR/NS15281951180
D min/max/mean-128.000127.00025.665

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Supplemental data

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Sample components

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Entire : Trypanosoma brucei cell

EntireName: Trypanosoma brucei cell
Components
  • Cell: Trypanosoma brucei cell

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Supramolecule #1: Trypanosoma brucei cell

SupramoleculeName: Trypanosoma brucei cell / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Trypanosoma brucei (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.2
GridModel: EMS lacey carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details2000-3000 cells/ml
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Electron Microsocpy Science / Diameter: 25 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 0.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 120

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