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- EMDB-46437: A 16-nm repeat of A-B Inner junction of TMT from the proximal reg... -

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Basic information

Entry
Database: EMDB / ID: EMD-46437
TitleA 16-nm repeat of A-B Inner junction of TMT from the proximal region of basal body, wild-type
Map data16-nm repeat of A-B inner junction from the proximal region of basal body, wild-type
Sample
  • Organelle or cellular component: Triplet and doublet microtubule from basal body and axoneme isolated from Tetrahymena thermophila
Keywordscilia / basal body / microtubule / CYTOSOLIC PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 9.82 Å
AuthorsLi S / Fernandez J / Ruehle M / Fabritius A / Pearson C / Agard DA / Winey M
Funding support United States, 3 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 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118099 United States
CitationJournal: EMBO J / Year: 2025
Title: The structure of basal body inner junctions from Tetrahymena revealed by electron cryo-tomography.
Authors: Sam Li / Jose-Jesus Fernandez / Marisa D Ruehle / Rachel A Howard-Till / Amy Fabritius / Chad G Pearson / David A Agard / Mark E Winey /
Abstract: The cilium is a microtubule-based eukaryotic organelle critical for many cellular functions. Its assembly initiates at a basal body and continues as an axoneme that projects out of the cell to form a ...The cilium is a microtubule-based eukaryotic organelle critical for many cellular functions. Its assembly initiates at a basal body and continues as an axoneme that projects out of the cell to form a functional cilium. This assembly process is tightly regulated. However, our knowledge of the molecular architecture and the mechanism of assembly is limited. By applying cryo-electron tomography, we obtained structures of the inner junction in three regions of the cilium from Tetrahymena: the proximal, the central core of the basal body, and the axoneme. We identified several protein components in the basal body. While a few proteins are distributed throughout the entire length of the organelle, many are restricted to specific regions, forming intricate local interaction networks in the inner junction and bolstering local structural stability. By examining the inner junction in a POC1 knockout mutant, we found the triplet microtubule was destabilized, resulting in a defective structure. Surprisingly, several axoneme-specific components were found to "infiltrate" into the mutant basal body. Our findings provide molecular insight into cilium assembly at the inner junctions, underscoring its precise spatial regulation.
History
DepositionAug 6, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46437.png

Downloads & links

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Map

FileDownload / File: emd_46437.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation16-nm repeat of A-B inner junction from the proximal region of basal body, wild-type
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067
Minimum - Maximum-0.21054293 - 0.25713998
Average (Standard dev.)0.0011556795 (±0.01739746)
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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Half map: half map 1, 16-nm repeat of A-B inner...

Fileemd_46437_half_map_1.map
Annotationhalf map 1, 16-nm repeat of A-B inner junction from the proximal region of basal body, wild-type
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2, 16-nm repeat of A-B inner...

Fileemd_46437_half_map_2.map
Annotationhalf map 2, 16-nm repeat of A-B inner junction from the proximal region of basal body, wild-type
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Triplet and doublet microtubule from basal body and axoneme isola...

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

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Supramolecule #1: Triplet and doublet microtubule from basal body and axoneme isola...

SupramoleculeName: Triplet and doublet microtubule from basal body and axoneme isolated from Tetrahymena thermophila
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
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
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 12290
ExtractionNumber tomograms: 93 / Number images used: 12290 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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