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- EMDB-10727: Electron cryo-tomography reconstruction and subvolume averaging o... -

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Basic information

Entry
Database: EMDB / ID: EMD-10727
TitleElectron cryo-tomography reconstruction and subvolume averaging of the A-C linker from the start of the proximal region of Paramecium tetraurelia basal body
Map data
Sample
  • Organelle or cellular component: Electron cryo-tomography reconstruction and subvolume averaging of the microtubule triplet from the start of the proximal region of Paramecium tetraurelia basal body
Biological speciesParamecium tetraurelia (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 31.2 Å
AuthorsGuichard P / Hamel V / Le Guennec M
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationPPOOP3_157517 Switzerland
European Research Council (ERC)715289 Switzerland
CitationJournal: EMBO J / Year: 2020
Title: Architecture of the centriole cartwheel-containing region revealed by cryo-electron tomography.
Authors: Nikolai Klena / Maeva Le Guennec / Anne-Marie Tassin / Hugo van den Hoek / Philipp S Erdmann / Miroslava Schaffer / Stefan Geimer / Gabriel Aeschlimann / Lubomir Kovacik / Yashar Sadian / ...Authors: Nikolai Klena / Maeva Le Guennec / Anne-Marie Tassin / Hugo van den Hoek / Philipp S Erdmann / Miroslava Schaffer / Stefan Geimer / Gabriel Aeschlimann / Lubomir Kovacik / Yashar Sadian / Kenneth N Goldie / Henning Stahlberg / Benjamin D Engel / Virginie Hamel / Paul Guichard /
Abstract: Centrioles are evolutionarily conserved barrels of microtubule triplets that form the core of the centrosome and the base of the cilium. While the crucial role of the proximal region in centriole ...Centrioles are evolutionarily conserved barrels of microtubule triplets that form the core of the centrosome and the base of the cilium. While the crucial role of the proximal region in centriole biogenesis has been well documented, its native architecture and evolutionary conservation remain relatively unexplored. Here, using cryo-electron tomography of centrioles from four evolutionarily distant species, we report on the architectural diversity of the centriole's proximal cartwheel-bearing region. Our work reveals that the cartwheel central hub is constructed from a stack of paired rings with cartwheel inner densities inside. In both Paramecium and Chlamydomonas, the repeating structural unit of the cartwheel has a periodicity of 25 nm and consists of three ring pairs, with 6 radial spokes emanating and merging into a single bundle that connects to the microtubule triplet via the D2-rod and the pinhead. Finally, we identified that the cartwheel is indirectly connected to the A-C linker through the triplet base structure extending from the pinhead. Together, our work provides unprecedented evolutionary insights into the architecture of the centriole proximal region, which underlies centriole biogenesis.
History
DepositionMar 4, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.69
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.69
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10727.png

Downloads & links

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Map

FileDownload / File: emd_10727.map.gz / Format: CCP4 / Size: 20.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.45 Å/pix.
x 73 pix.
= 251.85 Å		3.45 Å/pix.
x 228 pix.
= 786.6 Å		3.45 Å/pix.
x 320 pix.
= 1104. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 3.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.69 / Movie #1: 1.69
Minimum - Maximum0.6213951 - 2.8956633
Average (Standard dev.)1.5554454 (±0.23920731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions22832073
Spacing32022873
CellA: 1104.0 Å / B: 786.60004 Å / C: 251.85 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.453.453.45
M x/y/z32022873
origin x/y/z0.0000.0000.000
length x/y/z1104.000786.600251.850
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS32022873
D min/max/mean0.6212.8961.555

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Supplemental data

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Sample components

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Entire : Electron cryo-tomography reconstruction and subvolume averaging o...

EntireName: Electron cryo-tomography reconstruction and subvolume averaging of the microtubule triplet from the start of the proximal region of Paramecium tetraurelia basal body
Components
  • Organelle or cellular component: Electron cryo-tomography reconstruction and subvolume averaging of the microtubule triplet from the start of the proximal region of Paramecium tetraurelia basal body

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Supramolecule #1: Electron cryo-tomography reconstruction and subvolume averaging o...

SupramoleculeName: Electron cryo-tomography reconstruction and subvolume averaging of the microtubule triplet from the start of the proximal region of Paramecium tetraurelia basal body
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Paramecium tetraurelia (eukaryote) / Organelle: Basal Body

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 31.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1042
ExtractionNumber tomograms: 1042 / Number images used: 14
Final angle assignmentType: OTHER / Details: Back Projection

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