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- EMDB-47819: Overall map of T. brucei 48 nm repeat FAP106B-KD -

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Basic information

Entry
Database: EMDB / ID: EMD-47819
TitleOverall map of T. brucei 48 nm repeat FAP106B-KD
Map data
Sample
  • Organelle or cellular component: Trypanosoma brucei flagellum with FAP106B-KD
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 / Hill KL / Zhou ZH
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
DepositionNov 8, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47819.png

Downloads & links

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Map

FileDownload / File: emd_47819.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 320 pix.
= 704. Å		2.2 Å/pix.
x 320 pix.
= 704. Å		2.2 Å/pix.
x 320 pix.
= 704. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.03911421 - 0.11133147
Average (Standard dev.)0.0015179175 (±0.010675619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 704.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47819_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47819_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Trypanosoma brucei flagellum with FAP106B-KD

EntireName: Trypanosoma brucei flagellum with FAP106B-KD
Components
  • Organelle or cellular component: Trypanosoma brucei flagellum with FAP106B-KD

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Supramolecule #1: Trypanosoma brucei flagellum with FAP106B-KD

SupramoleculeName: Trypanosoma brucei flagellum with FAP106B-KD / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Macromolecule list: #60, #59, #51-#52, #56-#58, #50, #55, #49, #54, #47-#48, #53, #46, #36, #38, #34, #37, #35, #41, #43, #42, #40, #44, #39, #45, #28, #21-#22, #20, #25, #16, #27, #26, #23, #19, ...Macromolecule list: #60, #59, #51-#52, #56-#58, #50, #55, #49, #54, #47-#48, #53, #46, #36, #38, #34, #37, #35, #41, #43, #42, #40, #44, #39, #45, #28, #21-#22, #20, #25, #16, #27, #26, #23, #19, #29, #32, #31, #30, #33, #8, #13, #12, #11, #10, #14, #9, #24, #18, #15, #17, #5-#7, #1-#4
Details: Demembraned flagella were split by mild protease treatment
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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM (ver. 4.1)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 9984 / 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: 1096054
Startup modelType of model: EMDB MAP
EMDB ID:

24664

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 68411
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 68411

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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