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- EMDB-47602: Focus refine map of T. brucei DMT 96 nm repeat radial spoke 3 base -

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Basic information

Entry
Database: EMDB / ID: EMD-47602
TitleFocus refine map of T. brucei DMT 96 nm repeat radial spoke 3 base
Map data
Sample
  • Organelle or cellular component: Trypanasoma brucei flagella
Keywordsflagella / microtubule / MOTOR PROTEIN
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsXia X / Shimogawa MM / Wang H / Liu S / Wijono A / Langousis G / Kassem AM / Wohlschlegel JA / Zhou ZH / Hill K
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI052348 United States
CitationJournal: Science / Year: 2025
Title: Trypanosome doublet microtubule structures reveal flagellum assembly and motility mechanisms.
Authors: Xian Xia / Michelle M Shimogawa / Hui Wang / Samuel Liu / Angeline Wijono / Gerasimos Langousis / Ahmad M Kassem / James A Wohlschlegel / Kent L Hill / Z Hong Zhou /
Abstract: The flagellum of drives the parasite's characteristic screw-like motion and is essential for its replication, transmission, and pathogenesis. However, the molecular details of this process remain ...The flagellum of drives the parasite's characteristic screw-like motion and is essential for its replication, transmission, and pathogenesis. However, the molecular details of this process remain unclear. Here, we present high-resolution (up to 2.8 angstrom) cryo-electron microscopy structures of flagellar doublet microtubules (DMTs). Integrated modeling identified 154 different axonemal proteins inside and outside the DMT and, together with genetic and proteomic interrogation, revealed conserved and trypanosome-specific foundations of flagellum assembly and motility. We captured axonemal dynein motors in their pre-power stroke state. Comparing atomic models between pre- and post-power strokes defined how dynein structural changes drive sliding of adjacent DMTs during flagellar beating. This study illuminates structural dynamics underlying flagellar motility and identifies pathogen-specific proteins to consider for therapeutic interventions targeting neglected diseases.
History
DepositionOct 31, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47602.png

Downloads & links

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Map

FileDownload / File: emd_47602.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.008116618 - 0.031237688
Average (Standard dev.)0.00042955118 (±0.0025328693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47602_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47602_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_47602_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trypanasoma brucei flagella

EntireName: Trypanasoma brucei flagella
Components
  • Organelle or cellular component: Trypanasoma brucei flagella

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Supramolecule #1: Trypanasoma brucei flagella

SupramoleculeName: Trypanasoma brucei flagella / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#261
Source (natural)Organism: Trypanosoma brucei brucei TREU927 (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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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: 2 / Number real images: 106694 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 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: 7830978
Startup modelType of model: EMDB MAP
EMDB ID:

24664

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 70118
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 244497 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL

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