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- EMDB-47681: Crithidia fasciculata doublet microtubule - ponticulus at positio... -

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Basic information

Entry
Database: EMDB / ID: EMD-47681
TitleCrithidia fasciculata doublet microtubule - ponticulus at position 2 within 48-nm repeat length
Map datasharpened map of ponticulus at position 2
Sample
  • Complex: doublet microtubules from Crithidia fasciculata
Keywordsaxoneme / parasite / trypanosomatids / Crithidia fasciculata / STRUCTURAL PROTEIN
Biological speciesCrithidia fasciculata (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsNiu Q / Zeng J / Zhang R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138854 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI179885 United States
CitationJournal: Science / Year: 2025
Title: Evolutionary adaptations of doublet microtubules in trypanosomatid parasites.
Authors: Matthew H Doran / Qingwei Niu / Jianwei Zeng / Tom Beneke / James Smith / Peter Ren / Sophia Fochler / Adrian Coscia / Johanna L Höög / Shimi Meleppattu / Polina V Lishko / Richard J ...Authors: Matthew H Doran / Qingwei Niu / Jianwei Zeng / Tom Beneke / James Smith / Peter Ren / Sophia Fochler / Adrian Coscia / Johanna L Höög / Shimi Meleppattu / Polina V Lishko / Richard J Wheeler / Eva Gluenz / Rui Zhang / Alan Brown /
Abstract: The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet ...The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet microtubules (DMTs). In this work, we present cryo-electron microscopy structures of DMTs from two trypanosomatid species, and , at resolutions up to 2.7 angstrom. The structures revealed 27 trypanosomatid-specific microtubule inner proteins, a specialized dynein-docking complex, and the presence of paralogous proteins that enable higher-order periodicities or proximal-distal patterning. Leveraging the genetic tractability of trypanosomatid species, we quantified the location and contribution of each structure-identified protein to swimming behavior. Our study shows that proper B-tubule closure is critical for flagellar motility, exemplifying how integrating structural identification with systematic gene deletion can dissect individual protein contributions to flagellar motility.
History
DepositionNov 3, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47681.png

Downloads & links

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Map

FileDownload / File: emd_47681.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of ponticulus at position 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 512 pix.
= 681.933 Å		1.33 Å/pix.
x 512 pix.
= 681.933 Å		1.33 Å/pix.
x 512 pix.
= 681.933 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3319 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.09406393 - 2.4993148
Average (Standard dev.)0.00046790674 (±0.016056485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 681.9328 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47681_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map of ponticulus at position 2

Fileemd_47681_additional_1.map
Annotationunsharpened map of ponticulus at position 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47681_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47681_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 : doublet microtubules from Crithidia fasciculata

EntireName: doublet microtubules from Crithidia fasciculata
Components
  • Complex: doublet microtubules from Crithidia fasciculata

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Supramolecule #1: doublet microtubules from Crithidia fasciculata

SupramoleculeName: doublet microtubules from Crithidia fasciculata / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Crithidia fasciculata (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
Details: 30 mM HEPES pH 7.4, 30 mM KCl, 0.5 mM EGTA, 1 mM DTT, Roche Protease Inhibitor
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 38511 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 970134
Startup modelType of model: EMDB MAP
EMDB ID:

40619

Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 43430
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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