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Yorodumi- EMDB-20014: T. Brucei Axoneme in DRC11-knockdown procyclic form revealed by c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20014 | |||||||||||||||||||||||||||||||||
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Title | T. Brucei Axoneme in DRC11-knockdown procyclic form revealed by cryo electron tomography with Volta phase plate. | |||||||||||||||||||||||||||||||||
Map data | DRC11-knock-down Axoneme of T.brucei in its procyclic form revealed by cryo electron tomography | |||||||||||||||||||||||||||||||||
Sample |
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Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 35.6 Å | |||||||||||||||||||||||||||||||||
Authors | Zhang J | |||||||||||||||||||||||||||||||||
Funding support | Switzerland, United States, 10 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20014.map.gz | 36.6 MB | EMDB map data format | |
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Header (meta data) | emd-20014-v30.xml emd-20014.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_20014.png | 96.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20014 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20014 | HTTPS FTP |
-Validation report
Summary document | emd_20014_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_20014_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_20014_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20014 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20014 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20014.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | DRC11-knock-down Axoneme of T.brucei in its procyclic form revealed by cryo electron tomography | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.103 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axo...
Entire | Name: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axoneme + paraflafellar Rod. |
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Components |
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-Supramolecule #1: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axo...
Supramolecule | Name: Flagellum skeleton of DRC11-knockdown procyclic form T.brucei axoneme + paraflafellar Rod. type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) / Organelle: Flagellum |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 35.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1726 |
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Extraction | Number tomograms: 19 / Number images used: 1726 |
Final angle assignment | Type: NOT APPLICABLE |