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- EMDB-4926: Microtubule triplet of isolated Paramecium tetraurelia centriole ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4926
TitleMicrotubule triplet of isolated Paramecium tetraurelia centriole - inner core
Map dataNone
Sample
  • Organelle or cellular component: Microtubule triplet from P. Tetraurelia isolated centriole.
Biological speciesParamecium tetraurelia (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 16.7 Å
AuthorsLe Guennec M / Klena N / Tassin AM / Van der Hoek H / Erdmann PS / Schaffer M / Kovacik L / Goldie KN / Stahlberg H / Engel BD ...Le Guennec M / Klena N / Tassin AM / Van der Hoek H / Erdmann PS / Schaffer M / Kovacik L / Goldie KN / Stahlberg H / Engel BD / Hamel V / Guichard P
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council715289 Switzerland
Swiss National Science FoundationPP00P3_157517 Switzerland
CitationJournal: Sci Adv / Year: 2020
Title: A helical inner scaffold provides a structural basis for centriole cohesion.
Authors: Maeva Le Guennec / Nikolai Klena / Davide Gambarotto / Marine H Laporte / Anne-Marie Tassin / Hugo van den Hoek / Philipp S Erdmann / Miroslava Schaffer / Lubomir Kovacik / Susanne Borgers / ...Authors: Maeva Le Guennec / Nikolai Klena / Davide Gambarotto / Marine H Laporte / Anne-Marie Tassin / Hugo van den Hoek / Philipp S Erdmann / Miroslava Schaffer / Lubomir Kovacik / Susanne Borgers / Kenneth N Goldie / Henning Stahlberg / Michel Bornens / Juliette Azimzadeh / Benjamin D Engel / Virginie Hamel / Paul Guichard /
Abstract: The ninefold radial arrangement of microtubule triplets (MTTs) is the hallmark of the centriole, a conserved organelle crucial for the formation of centrosomes and cilia. Although strong cohesion ...The ninefold radial arrangement of microtubule triplets (MTTs) is the hallmark of the centriole, a conserved organelle crucial for the formation of centrosomes and cilia. Although strong cohesion between MTTs is critical to resist forces applied by ciliary beating and the mitotic spindle, how the centriole maintains its structural integrity is not known. Using cryo-electron tomography and subtomogram averaging of centrioles from four evolutionarily distant species, we found that MTTs are bound together by a helical inner scaffold covering ~70% of the centriole length that maintains MTTs cohesion under compressive forces. Ultrastructure Expansion Microscopy (U-ExM) indicated that POC5, POC1B, FAM161A, and Centrin-2 localize to the scaffold structure along the inner wall of the centriole MTTs. Moreover, we established that these four proteins interact with each other to form a complex that binds microtubules. Together, our results provide a structural and molecular basis for centriole cohesion and geometry.
History
DepositionMay 2, 2019-
Header (metadata) releaseFeb 26, 2020-
Map releaseFeb 26, 2020-
UpdateMar 11, 2020-
Current statusMar 11, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.67
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.67
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4926.png

Downloads & links

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Map

FileDownload / File: emd_4926.map.gz / Format: CCP4 / Size: 31.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 3.45 Å
Density
Contour LevelBy AUTHOR: 1.67 / Movie #1: 1.67
Minimum - Maximum-0.1417222 - 3.4374585
Average (Standard dev.)1.4973092 (±0.3206919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions28828899
Spacing28828899
CellA: 993.60004 Å / B: 993.60004 Å / C: 341.55002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.453.453.45
M x/y/z28828899
origin x/y/z0.0000.0000.000
length x/y/z993.600993.600341.550
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS28828899
D min/max/mean-0.1423.4371.497

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Supplemental data

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Sample components

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Entire : Microtubule triplet from P. Tetraurelia isolated centriole.

EntireName: Microtubule triplet from P. Tetraurelia isolated centriole.
Components
  • Organelle or cellular component: Microtubule triplet from P. Tetraurelia isolated centriole.

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Supramolecule #1: Microtubule triplet from P. Tetraurelia isolated centriole.

SupramoleculeName: Microtubule triplet from P. Tetraurelia isolated centriole.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: This map corresponds to the microtubule triplet structure located at the inner core of the centriole
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 / Instrument: HOMEMADE PLUNGER

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Electron microscopy

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

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Image processing

ExtractionNumber tomograms: 14 / Number images used: 1693
Final angle assignmentType: OTHER / Details: Back projection
Final reconstructionApplied symmetry - Point group: C9 (9 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1693
FSC plot (resolution estimation)

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