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- EMDB-11049: Electron cryo-tomography reconstruction and subvolume averaging o... -

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Basic information

Entry
Database: EMDB / ID: EMD-11049
TitleElectron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from Trichonympha
Map data
Sample
  • Organelle or cellular component: Isolated Trichonmypha centriole
Biological speciesTrichonympha sp. (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 42.0 Å
AuthorsGuichard P / Hachet V / Majubu N / Neves A / Demurtas D / Olieric N / Fluckiger I / Yamada A / Kihara K / Nishida Y ...Guichard P / Hachet V / Majubu N / Neves A / Demurtas D / Olieric N / Fluckiger I / Yamada A / Kihara K / Nishida Y / Moriya S / Steinmetz MO / Hongoh Y / Gonczy P
CitationJournal: Curr Biol / Year: 2013
Title: Native architecture of the centriole proximal region reveals features underlying its 9-fold radial symmetry.
Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu ...Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu Moriya / Michel O Steinmetz / Yuichi Hongoh / Pierre Gönczy /
Abstract: BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel ...BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel that dictates the 9-fold symmetry of centrioles. Although the cartwheel architecture has been recently analyzed, how it connects to the peripheral microtubules is not understood. More generally, a high-resolution view of the proximal region of the centriole is lacking, thus limiting understanding of the underlying assembly mechanisms.
RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the ...RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the cartwheel that exhibit a 9-fold symmetrical arrangement, as well as the structure of the Pinhead and the A-C linker that connect to microtubules. Moreover, we uncover striking chiral features that might impart directionality to the entire centriole. Furthermore, we identify Trichonympha SAS-6 and demonstrate that it localizes to the cartwheel in vivo.
CONCLUSIONS: Our work provides unprecedented insight into the architecture of the centriole proximal region, which is key for a thorough understanding of the mechanisms governing centriole assembly.
History
DepositionMay 18, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateMay 27, 2020-
Current statusMay 27, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.33
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11049.png

Downloads & links

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Map

FileDownload / File: emd_11049.map.gz / Format: CCP4 / Size: 3.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 7.5 Å
Density
Contour LevelBy AUTHOR: 3.33 / Movie #1: 3.33
Minimum - Maximum0.3161099 - 5.953592
Average (Standard dev.)2.5933013 (±0.93229675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions12411166
Spacing11112466
CellA: 832.5 Å / B: 930.0 Å / C: 495.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.57.57.5
M x/y/z11112466
origin x/y/z0.0000.0000.000
length x/y/z832.500930.000495.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS11112466
D min/max/mean0.3165.9542.593

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Supplemental data

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Sample components

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Entire : Isolated Trichonmypha centriole

EntireName: Isolated Trichonmypha centriole
Components
  • Organelle or cellular component: Isolated Trichonmypha centriole

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Supramolecule #1: Isolated Trichonmypha centriole

SupramoleculeName: Isolated Trichonmypha centriole / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Trichonympha sp. (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 80.0 e/Å2 / Details: binning 2, 0.748 nm final pixel size

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Image processing

ExtractionNumber tomograms: 6 / Number images used: 6000
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C9 (9 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 42.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 6000

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