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- EMDB-20014: T. Brucei Axoneme in DRC11-knockdown procyclic form revealed by c... -

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Basic information

Entry
Database: EMDB / ID: EMD-20014
TitleT. Brucei Axoneme in DRC11-knockdown procyclic form revealed by cryo electron tomography with Volta phase plate.
Map dataDRC11-knock-down Axoneme of T.brucei in its procyclic form revealed by cryo electron tomography
Sample
  • Organelle or cellular component: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axoneme + paraflafellar Rod.
Biological speciesTrypanosoma brucei brucei (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 35.6 Å
AuthorsZhang J
Funding support Switzerland, United States, 10 items
OrganizationGrant numberCountry
Swiss National Science FoundationP2BEP3_162094 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI052348 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
Swiss National Science FoundationP300PA_174358 Switzerland
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Elife / Year: 2019
Title: Cryo electron tomography with volta phase plate reveals novel structural foundations of the 96-nm axonemal repeat in the pathogen .
Authors: Simon Imhof / Jiayan Zhang / Hui Wang / Khanh Huy Bui / Hoangkim Nguyen / Ivo Atanasov / Wong H Hui / Shun Kai Yang / Z Hong Zhou / Kent L Hill /
Abstract: The 96-nm axonemal repeat includes dynein motors and accessory structures as the foundation for motility of eukaryotic flagella and cilia. However, high-resolution 3D axoneme structures are ...The 96-nm axonemal repeat includes dynein motors and accessory structures as the foundation for motility of eukaryotic flagella and cilia. However, high-resolution 3D axoneme structures are unavailable for organisms among the Excavates, which include pathogens of medical and economic importance. Here we report cryo electron tomography structures of the 96-nm repeat from , a protozoan parasite in the Excavate lineage that causes African trypanosomiasis. We examined bloodstream and procyclic life cycle stages, and a knockdown lacking DRC11/CMF22 of the nexin dynein regulatory complex (NDRC). Sub-tomogram averaging yields a resolution of 21.8 Å for the 96-nm repeat. We discovered several lineage-specific structures, including novel inter-doublet linkages and microtubule inner proteins (MIPs). We establish that DRC11/CMF22 is required for the NDRC proximal lobe that binds the adjacent doublet microtubule. We propose that lineage-specific elaboration of axoneme structure in reflects adaptations to support unique motility needs in diverse host environments.
History
DepositionMar 20, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseDec 11, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_20014.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDRC11-knock-down Axoneme of T.brucei in its procyclic form revealed by cryo electron tomography
Voxel sizeX=Y=Z: 6.103 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-4.0754213 - 6.051994
Average (Standard dev.)-0.00000715469 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions220220220
Spacing220220220
CellA=B=C: 1342.66 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.1036.1036.103
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z1342.6601342.6601342.660
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS-110-110-110
NC/NR/NS220220220
D min/max/mean-4.0756.052-0.000

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Supplemental data

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Sample components

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Entire : Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axo...

EntireName: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axoneme + paraflafellar Rod.
Components
  • Organelle or cellular component: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axoneme + paraflafellar Rod.

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Supramolecule #1: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axo...

SupramoleculeName: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axoneme + paraflafellar Rod.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Organelle: Flagellum

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 19 / Number images used: 1726
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 35.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1726

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