EMDB-10726: Electron cryo-tomography reconstruction and subvolume averaging o...

Basic information

• Entry: Database: EMDB / ID: EMD-10726
• Title: Electron cryo-tomography reconstruction and subvolume averaging of the A-C linker from the end of the proximal region of Paramecium tetraurelia basal body

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 species: Paramecium tetraurelia (eukaryote)
• Method: subtomogram averaging / cryo EM / Resolution: 31.2 Å
• Authors: Guichard P / Hamel V / Le Guennec M

Funding support

Switzerland, 2 items

Organization	Grant number	Country
Swiss National Science Foundation	PPOOP3_157517	Switzerland
European Research Council (ERC)	715289	Switzerland

• Citation: Journal: 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 / 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 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

Deposition	Mar 4, 2020	-
Header (metadata) release	Oct 14, 2020	-
Map release	Oct 14, 2020	-
Update	Apr 14, 2021	-
Current status	Apr 14, 2021	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_10726.map.gz / Format: CCP4 / Size: 20.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 3.45 Å

Density

Contour Level	By AUTHOR: 1.07 / Movie #1: 1.07
Minimum - Maximum	0.41080713 - 1.5893039
Average (Standard dev.)	0.8766873 (±0.16682352)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 230 320 73 Spacing 320 230 73
Cell	A: 1104.0 Å / B: 793.5 Å / C: 251.85 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	3.45	3.45	3.45
M x/y/z	320	230	73
origin x/y/z	0.000	0.000	0.000
length x/y/z	1104.000	793.500	251.850
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	320	230	73
D min/max/mean	0.411	1.589	0.877

Supplemental data

Sample components

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

• Entire: Name: 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

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

• Supramolecule: Name: 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

Experimental details

Structure determination

• Method: cryo EM
• Processing: subtomogram averaging
• Aggregation state: cell

Sample preparation

• Buffer: pH: 7.2
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Extraction: Number tomograms: 899 / Number images used: 14
• Final angle assignment: Type: OTHER / Details: Back Projection
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 31.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 899