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- EMDB-74424: 8 nm Cartwheel Central Hub from Trichonympha spp. -

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Basic information

Entry
Database: EMDB / ID: EMD-74424
Title8 nm Cartwheel Central Hub from Trichonympha spp.
Map dataMap of 8nm cartwheel ring repeat from Trichonympha spp. proximal centriole
Sample
  • Organelle or cellular component: 8 nm Cartwheel Central Hub from the Proximal Centriole of Trichonympha spp.
    • Other: Cartwheel Assembly of T. agilis SAS-6
KeywordsTrichonympha / Centriole / Cartwheel / Tetramer / STRUCTURAL PROTEIN
Function / homologySpindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / centrosome / Spindle assembly abnormal 6
Function and homology information
Biological speciesTrichonympha (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 10.9 Å
AuthorsRowsell CM / Arin A / Bui KH
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-156354 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04774 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
DepositionDec 11, 2025-
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_74424.png

Downloads & links

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Map

FileDownload / File: emd_74424.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of 8nm cartwheel ring repeat from Trichonympha spp. proximal centriole
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 164 pix.
= 695.36 Å		4.24 Å/pix.
x 164 pix.
= 695.36 Å		4.24 Å/pix.
x 164 pix.
= 695.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.281
Minimum - Maximum-0.63312316 - 0.6934888
Average (Standard dev.)0.008884577 (±0.072237924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions164164164
Spacing164164164
CellA=B=C: 695.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74424_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of 8nm cartwheel ring repeat from...

Fileemd_74424_half_map_1.map
AnnotationHalf map of 8nm cartwheel ring repeat from Trichonympha spp. proximal centriole
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of 8nm cartwheel ring repeat from...

Fileemd_74424_half_map_2.map
AnnotationHalf map of 8nm cartwheel ring repeat from Trichonympha spp. proximal centriole
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 8 nm Cartwheel Central Hub from the Proximal Centriole of Trichon...

EntireName: 8 nm Cartwheel Central Hub from the Proximal Centriole of Trichonympha spp.
Components
  • Organelle or cellular component: 8 nm Cartwheel Central Hub from the Proximal Centriole of Trichonympha spp.
    • Other: Cartwheel Assembly of T. agilis SAS-6

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Supramolecule #1: 8 nm Cartwheel Central Hub from the Proximal Centriole of Trichon...

SupramoleculeName: 8 nm Cartwheel Central Hub from the Proximal Centriole of Trichonympha spp.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Subunit of the proximal centriole cartwheel of Trichonympha spp., isolated from the hindgut of Z. angusticollis.
Source (natural)Organism: Trichonympha (eukaryote) / Organelle: Centriole

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Macromolecule #1: Cartwheel Assembly of T. agilis SAS-6

MacromoleculeName: Cartwheel Assembly of T. agilis SAS-6 / type: other / ID: 1 / Details: Cartwheel Assembly of T. agilis SAS-6 / Classification: other
Source (natural)Organism: Trichonympha (eukaryote)
SequenceString:
MNQGDFDIRV STIVCLENGR KEERRLRYKF HQSFSIISSD ITFCLQITDS KNPKFLFDSI ISNSLFHDMH ESQYLLFEFY DFCQILSSYF EKCNKDEDYS VLIDESFPVL IVQQTTDYRI LSLLTIQLQK ANNERLTQYL IDRIQYFQRK TIDLKVSTDN

UniProtKB: Spindle assembly abnormal 6

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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 / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C9 (9 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 5), M) / Number subtomograms used: 6523
ExtractionNumber tomograms: 61 / Number images used: 6523 / 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)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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