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- EMDB-4929: Junction between microtubules triplets of in situ Chlamydomonas r... -

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Basic information

Entry
Database: EMDB / ID: EMD-4929
TitleJunction between microtubules triplets of in situ Chlamydomonas reinardtii centriole - inner core region
Map dataNone
Sample
  • Organelle or cellular component: Junction betweeen adjacent microtubules triplets from Chlamydomonas reinhardtii
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 31.1 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 3, 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: 0.991
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.991
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4929.png

Downloads & links

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Map

FileDownload / File: emd_4929.map.gz / Format: CCP4 / Size: 29.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 98 pix.
= 335.16 Å		3.42 Å/pix.
x 280 pix.
= 957.6 Å		3.42 Å/pix.
x 280 pix.
= 957.6 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: 3.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.991 / Movie #1: 0.991
Minimum - Maximum-0.15925741 - 1.6853378
Average (Standard dev.)0.7685138 (±0.1810984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions28028098
Spacing28028098
CellA: 957.60004 Å / B: 957.60004 Å / C: 335.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z28028098
origin x/y/z0.0000.0000.000
length x/y/z957.600957.600335.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS28028098
D min/max/mean-0.1591.6850.769

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Supplemental data

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Sample components

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Entire : Junction betweeen adjacent microtubules triplets from Chlamydomon...

EntireName: Junction betweeen adjacent microtubules triplets from Chlamydomonas reinhardtii
Components
  • Organelle or cellular component: Junction betweeen adjacent microtubules triplets from Chlamydomonas reinhardtii

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Supramolecule #1: Junction betweeen adjacent microtubules triplets from Chlamydomon...

SupramoleculeName: Junction betweeen adjacent microtubules triplets from Chlamydomonas reinhardtii
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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-PROPANE

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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: FLOOD BEAM / 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: 31.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 682
ExtractionNumber tomograms: 682 / Number images used: 5
Final angle assignmentType: OTHER / Details: Back projection
FSC plot (resolution estimation)

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