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- EMDB-47613: Leishmania tarentolae 48 nm doublet microtubule protofilament 2.2... -

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Basic information

Entry
Database: EMDB / ID: EMD-47613
TitleLeishmania tarentolae 48 nm doublet microtubule protofilament 2.2 focused refinement
Map dataDeepemhancer map of the Leishmania tarentolae 48 nm doublet microtubule protofilament 2.2 focused refinement
Sample
  • Complex: 48-nm structure of the Leishmania tarentolae doublet microtubule
Keywordsflagella / parasite / axoneme / doublet microtubule / STRUCTURAL PROTEIN
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDoran MH / Brown A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143183 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
DepositionOct 31, 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_47613.png

Downloads & links

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Map

FileDownload / File: emd_47613.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepemhancer map of the Leishmania tarentolae 48 nm doublet microtubule protofilament 2.2 focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 512 pix.
= 680.96 Å		1.33 Å/pix.
x 512 pix.
= 680.96 Å		1.33 Å/pix.
x 512 pix.
= 680.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0023135561 - 1.9216037
Average (Standard dev.)0.0005470628 (±0.017483002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 680.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Relion postprocessed map of the Leishmania tarentolae 48...

Fileemd_47613_additional_1.map
AnnotationRelion postprocessed map of the Leishmania tarentolae 48 nm doublet microtubule protofilament 2.2 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Relion reconstruction of the Leishmania tarentolae 48 nm...

Fileemd_47613_additional_2.map
AnnotationRelion reconstruction of the Leishmania tarentolae 48 nm doublet microtubule protofilament 2.2 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the Leishmania tarentolae 48...

Fileemd_47613_half_map_1.map
AnnotationHalf map 1 of the Leishmania tarentolae 48 nm doublet microtubule protofilament 2.2 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the Leishmania tarentolae 48...

Fileemd_47613_half_map_2.map
AnnotationHalf map 2 of the Leishmania tarentolae 48 nm doublet microtubule protofilament 2.2 focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 48-nm structure of the Leishmania tarentolae doublet microtubule

EntireName: 48-nm structure of the Leishmania tarentolae doublet microtubule
Components
  • Complex: 48-nm structure of the Leishmania tarentolae doublet microtubule

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Supramolecule #1: 48-nm structure of the Leishmania tarentolae doublet microtubule

SupramoleculeName: 48-nm structure of the Leishmania tarentolae doublet microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#86
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Organelle: Flagella

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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

Concentration6.5 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample consisted of freshly splayed Leishmania tarentolae axonemes.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

20631


Details: The map used for initial angular assignment is the C. reinhardtii DMT.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 533420
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: integrative model
Details: The initial model consisted of rigid body fit AlphaFold models and models build with ModelAngelo.

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