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- EMDB-42781: Triplet microtubule from the proximal region of basal body, focus... -

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Basic information

Entry
Database: EMDB / ID: EMD-42781
TitleTriplet microtubule from the proximal region of basal body, focusing on the B/C inner junction, wildtype Tetrahymena themorphila
Map datatriplet microtubule from the proximal region of basal body, focusing on the B/C inner junction, wildtype Tetrahymena thermophila
Sample
  • Organelle or cellular component: Triplet microtubule from basal body isolated from Tetrahymena thermophila
Keywordscilia / basal body / microtubule / CYTOSOLIC PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 Å
AuthorsRuehle M / Li S / Agard DA / Pearson C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140813 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127571-05A1 United States
CitationJournal: J Cell Biol / Year: 2024
Title: Poc1 bridges basal body inner junctions to promote triplet microtubule integrity and connections.
Authors: Marisa D Ruehle / Sam Li / David A Agard / Chad G Pearson /
Abstract: Basal bodies (BBs) are conserved eukaryotic structures that organize cilia. They are comprised of nine, cylindrically arranged, triplet microtubules (TMTs) connected to each other by inter-TMT ...Basal bodies (BBs) are conserved eukaryotic structures that organize cilia. They are comprised of nine, cylindrically arranged, triplet microtubules (TMTs) connected to each other by inter-TMT linkages which stabilize the structure. Poc1 is a conserved protein important for BB structural integrity in the face of ciliary forces transmitted to BBs. To understand how Poc1 confers BB stability, we identified the precise position of Poc1 in the Tetrahymena BB and the effect of Poc1 loss on BB structure. Poc1 binds at the TMT inner junctions, stabilizing TMTs directly. From this location, Poc1 also stabilizes inter-TMT linkages throughout the BB, including the cartwheel pinhead and the inner scaffold. The full localization of the inner scaffold protein Fam161A requires Poc1. As ciliary forces are increased, Fam161A is reduced, indicative of a force-dependent molecular remodeling of the inner scaffold. Thus, while not essential for BB assembly, Poc1 promotes BB interconnections that establish an architecture competent to resist ciliary forces.
History
DepositionNov 10, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42781.png

Downloads & links

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Map

FileDownload / File: emd_42781.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtriplet microtubule from the proximal region of basal body, focusing on the B/C inner junction, wildtype Tetrahymena thermophila
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 160 pix.
= 432. Å		2.7 Å/pix.
x 160 pix.
= 432. Å		2.7 Å/pix.
x 160 pix.
= 432. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.101
Minimum - Maximum-0.28644758 - 0.39625692
Average (Standard dev.)0.0014904169 (±0.025378551)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42781_msk_1.map
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Half map: #1

Fileemd_42781_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_42781_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Triplet microtubule from basal body isolated from Tetrahymena the...

EntireName: Triplet microtubule from basal body isolated from Tetrahymena thermophila
Components
  • Organelle or cellular component: Triplet microtubule from basal body isolated from Tetrahymena thermophila

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Supramolecule #1: Triplet microtubule from basal body isolated from Tetrahymena the...

SupramoleculeName: Triplet microtubule from basal body isolated from Tetrahymena thermophila
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (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: 7.5 / Details: 1xTE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K / Max: 78.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 2 / Average exposure time: 0.36 sec. / Average electron dose: 1.33 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 5071
ExtractionNumber tomograms: 61 / Number images used: 7938 / Software - Name: SPIDER
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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