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- EMDB-72601: Leishmania 96 nm half 2 protofilament refinement position 3_3 -

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Basic information

Entry
Database: EMDB / ID: EMD-72601
TitleLeishmania 96 nm half 2 protofilament refinement position 3_3
Map dataDeepEMhancer sharpened map
Sample
  • Complex: Leishmania 96 nm half 2 protofilament refinement position 3_3
Keywordsflagella / parasite / axoneme / doublet microtubule / STRUCTURAL PROTEIN
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDoran MH / Brown A
Funding support United States, 3 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
National Science Foundation (NSF, United States)MCB-2434879 United States
CitationJournal: bioRxiv / Year: 2025
Title: Axonemal dynein contributions to flagellar beat types and waveforms.
Authors: Sophia Fochler / Matthew H Doran / Tom Beneke / James Smith / Cecile Fort / Benjamin J Walker / Alan Brown / Eva Gluenz / Richard J Wheeler /
Abstract: Eukaryotic flagella, or motile cilia, are iconic molecular machines whose beating drives cell propulsion and fluid transport across diverse organisms. Beat type and waveform are tailored to function, ...Eukaryotic flagella, or motile cilia, are iconic molecular machines whose beating drives cell propulsion and fluid transport across diverse organisms. Beat type and waveform are tailored to function, differing between species and cell types, and individual flagella can switch between beat types. Aberrant beating causes ciliopathies and infertility in humans and prevents unicellular parasite transmission. Eight distinct dynein motor protein complexes bind to axonemal doublet microtubules (DMTs) within flagella and drive beating, yet despite extensive structural analysis, how this machinery achieves different beat types is unknown. Here, using the flagellate unicellular parasite , we show a division of labour where specific dyneins drive specific beat types. Using cryo-EM, we determined the structure of the 96-nm repeat unit of the DMT and identified its dynein composition. We used CRISPR-Cas9 to systematically delete all 96-nm repeat proteins, comprehensively mapping necessity for swimming, and determined the contribution of each dynein to incidence and waveform of the preferred beat types. Outer dynein arms (ODAs) were required for symmetric tip-to-base beats, specific single-headed inner dynein arms (IDAs) were important for asymmetric base-to-tip beats (IDA), and double-headed IDA important for both. This systematic analysis indicates that the prevailing dogma that ODAs drive and IDAs shape the beat is either incomplete or not universal, and establishes new hypotheses for how different species, cell types and individual flagella achieve their necessary beat types.
History
DepositionSep 8, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72601.png

Downloads & links

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Map

FileDownload / File: emd_72601.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
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: 0.317
Minimum - Maximum-0.0065623196 - 2.1573424
Average (Standard dev.)0.00062772824 (±0.018585643)
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 sharpened map

Fileemd_72601_additional_1.map
AnnotationRelion sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_72601_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_72601_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Leishmania 96 nm half 2 protofilament refinement position 3_3

EntireName: Leishmania 96 nm half 2 protofilament refinement position 3_3
Components
  • Complex: Leishmania 96 nm half 2 protofilament refinement position 3_3

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Supramolecule #1: Leishmania 96 nm half 2 protofilament refinement position 3_3

SupramoleculeName: Leishmania 96 nm half 2 protofilament refinement position 3_3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#313
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: P10 / 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) / Number grids imaged: 4 / Number real images: 37665 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 281984
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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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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