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- EMDB-5302: Trypanosoma brucei flagellum: axoneme -

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Basic information

Entry
Database: EMDB / ID: EMD-5302
TitleTrypanosoma brucei flagellum: axoneme
Map dataSub-tomogram average of the axoneme of Trypanosoma brucei
Sample
  • Sample: Trypanosoma brucei flagellum - axoneme
  • Organelle or cellular component: axoneme
Keywordsaxoneme
Biological speciesTrypanosoma brucei (eukaryote)
Methodsubtomogram averaging / cryo EM
AuthorsKoyfman AY / Schmid MF / Gheiratmand L / Fu CJ / Khant HA / Huang D / He CY / Chiu W
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Structure of Trypanosoma brucei flagellum accounts for its bihelical motion.
Authors: Alexey Y Koyfman / Michael F Schmid / Ladan Gheiratmand / Caroline J Fu / Htet A Khant / Dandan Huang / Cynthia Y He / Wah Chiu /
Abstract: Trypanosoma brucei is a parasitic protozoan that causes African sleeping sickness. It contains a flagellum required for locomotion and viability. In addition to a microtubular axoneme, the flagellum ...Trypanosoma brucei is a parasitic protozoan that causes African sleeping sickness. It contains a flagellum required for locomotion and viability. In addition to a microtubular axoneme, the flagellum contains a crystalline paraflagellar rod (PFR) and connecting proteins. We show here, by cryoelectron tomography, the structure of the flagellum in three bending states. The PFR lattice in straight flagella repeats every 56 nm along the length of the axoneme, matching the spacing of the connecting proteins. During flagellar bending, the PFR crystallographic unit cell lengths remain constant while the interaxial angles vary, similar to a jackscrew. The axoneme drives the expansion and compression of the PFR lattice. We propose that the PFR modifies the in-plane axoneme motion to produce the characteristic trypanosome bihelical motility as captured by high-speed light microscope videography.
History
DepositionJun 8, 2011-
Header (metadata) releaseJun 21, 2011-
Map releaseJun 21, 2011-
UpdateJun 5, 2013-
Current statusJun 5, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5302_1.png

Downloads & links

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Map

FileDownload / File: emd_5302.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of the axoneme of Trypanosoma brucei
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.6 Å/pix.
x 256 pix.
= 2713.6 Å		10.6 Å/pix.
x 256 pix.
= 2713.6 Å		10.6 Å/pix.
x 256 pix.
= 2713.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-4.93383121 - 7.60374546
Average (Standard dev.)0.00011207 (±0.99792266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-213-231-168
Dimensions256256256
Spacing256256256
CellA=B=C: 2713.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.610.610.6
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z2713.6002713.6002713.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-231-213-168
NC/NR/NS256256256
D min/max/mean-4.9347.6040.000

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Supplemental data

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Sample components

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Entire : Trypanosoma brucei flagellum - axoneme

EntireName: Trypanosoma brucei flagellum - axoneme
Components
  • Sample: Trypanosoma brucei flagellum - axoneme
  • Organelle or cellular component: axoneme

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Supramolecule #1000: Trypanosoma brucei flagellum - axoneme

SupramoleculeName: Trypanosoma brucei flagellum - axoneme / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: axoneme

SupramoleculeName: axoneme / type: organelle_or_cellular_component / ID: 1 / Name.synonym: axoneme / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Trypanosoma brucei (eukaryote) / synonym: Trypanosome / Organelle: flagellum / Location in cell: flagellum

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferDetails: PBS
GridDetails: 200 mesh gold grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot III / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2100
DateJun 25, 2008
Image recordingAverage electron dose: 70 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 15000
Sample stageSpecimen holder: 60 degree / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

DetailsAverage number of tilts used in the 3D reconstructions: 60. Average tomographic tilt angle increment: 2.
Final reconstructionSoftware - Name: IMOD

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