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- EMDB-76289: 16nm Microtubule Triplet from Trichonympha spp. -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-76289
Title16nm Microtubule Triplet from Trichonympha spp.
Map data
Sample
  • Organelle or cellular component: Centriole
KeywordsCentriole / basal body / cryo-EM / Subtomogram averaging / STRUCTURAL PROTEIN
Biological speciesTrichonympha sp. (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 14.4 Å
AuthorsRowsell CM / Arin A / Bui KH
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-156354 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: The Native Structure of the Trichonympha Centriole Cartwheel Reveals a Zig-Zag Stacking Pattern
Authors: Rowsell CM / Arin A / Bui KH
History
DepositionMar 25, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76289.png

Downloads & links

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Map

FileDownload / File: emd_76289.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.3 Å/pix.
x 160 pix.
= 1008. Å		6.3 Å/pix.
x 160 pix.
= 1008. Å		6.3 Å/pix.
x 160 pix.
= 1008. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.335
Minimum - Maximum-0.5585232 - 1.1420501
Average (Standard dev.)0.01705781 (±0.106395856)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 1008.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76289_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76289_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76289_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Centriole

EntireName: Centriole
Components
  • Organelle or cellular component: Centriole

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Supramolecule #1: Centriole

SupramoleculeName: Centriole / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Trichonympha sp. (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris Buffer
1.0 mMEDTAEDTA

Details: TE Buffer: 10mM Tris pH 8, 1mM EDTA pH 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: Grid was plasma discharged prior to use
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsSample was cross-linked with gluteraldehyde (0.15% final concentration)

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 1 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 5.0), M) / Number subtomograms used: 1117
ExtractionNumber tomograms: 81 / Number images used: 1117 / Software - Name: Warp (ver. 2.0)
CTF correctionSoftware - Name: Warp (ver. 2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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