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Yorodumi- EMDB-23619: Sub-tomographic averaged structure of the paracrystalline PFR dis... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23619 | |||||||||||||||||||||||||||||||||
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Title | Sub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei | |||||||||||||||||||||||||||||||||
Map data | The unmasked sub-tomographic averaging result of the PFR distal zone of T. brucei, after low pass filtering to 30 Angstrom | |||||||||||||||||||||||||||||||||
Sample |
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Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 28.5 Å | |||||||||||||||||||||||||||||||||
Authors | Zhang J / Wang H | |||||||||||||||||||||||||||||||||
Funding support | United States, Switzerland, 10 items
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Citation | Journal: Cell Discov / Year: 2021 Title: Structure of the trypanosome paraflagellar rod and insights into non-planar motility of eukaryotic cells. Authors: Jiayan Zhang / Hui Wang / Simon Imhof / Xueting Zhou / Shiqing Liao / Ivo Atanasov / Wong H Hui / Kent L Hill / Z Hong Zhou / Abstract: Eukaryotic flagella (synonymous with cilia) rely on a microtubule-based axoneme, together with accessory filaments to carryout motility and signaling functions. While axoneme structures are well ...Eukaryotic flagella (synonymous with cilia) rely on a microtubule-based axoneme, together with accessory filaments to carryout motility and signaling functions. While axoneme structures are well characterized, 3D ultrastructure of accessory filaments and their axoneme interface are mostly unknown, presenting a critical gap in understanding structural foundations of eukaryotic flagella. In the flagellum of the protozoan parasite Trypanosoma brucei (T. brucei), the axoneme is accompanied by a paraflagellar rod (PFR) that supports non-planar motility and signaling necessary for disease transmission and pathogenesis. Here, we employed cryogenic electron tomography (cryoET) with sub-tomographic averaging, to obtain structures of the PFR, PFR-axoneme connectors (PACs), and the axonemal central pair complex (CPC). The structures resolve how the 8 nm repeat of the axonemal tubulin dimer interfaces with the 54 nm repeat of the PFR, which consist of proximal, intermediate, and distal zones. In the distal zone, stacked "density scissors" connect with one another to form a "scissors stack network (SSN)" plane oriented 45° to the axoneme axis; and ~370 parallel SSN planes are connected by helix-rich wires into a paracrystalline array with ~90% empty space. Connections from these wires to the intermediate zone, then to overlapping layers of the proximal zone and to the PACs, and ultimately to the CPC, point to a contiguous pathway for signal transmission. Together, our findings provide insights into flagellum-driven, non-planar helical motility of T. brucei and have broad implications ranging from cell motility and tensegrity in biology, to engineering principles in bionics. | |||||||||||||||||||||||||||||||||
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_23619.map.gz | 252.2 MB | EMDB map data format | |
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Header (meta data) | emd-23619-v30.xml emd-23619.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_23619.png | 279.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23619 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23619 | HTTPS FTP |
-Validation report
Summary document | emd_23619_validation.pdf.gz | 402.2 KB | Display | EMDB validaton report |
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Full document | emd_23619_full_validation.pdf.gz | 401.7 KB | Display | |
Data in XML | emd_23619_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_23619_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23619 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23619 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23619.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The unmasked sub-tomographic averaging result of the PFR distal zone of T. brucei, after low pass filtering to 30 Angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.106 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 : Sub-tomographic averaged structure of the paracrystalline PFR dis...
Entire | Name: Sub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei |
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Components |
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-Supramolecule #1: Sub-tomographic averaged structure of the paracrystalline PFR dis...
Supramolecule | Name: Sub-tomographic averaged structure of the paracrystalline PFR distal zone in T. brucei 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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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 | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 28.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1362 |
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Extraction | Number tomograms: 12 / Number images used: 1362 |
Final angle assignment | Type: NOT APPLICABLE |