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Yorodumi- EMDB-11384: Treponema denticola chemotaxis signalling arrays in an ODP (TDE24... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11384 | |||||||||
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Title | Treponema denticola chemotaxis signalling arrays in an ODP (TDE2498) and TDE2496 deletion mutant | |||||||||
Map data | Treponema denticola arrays in an ODP (TDE2498) and TDE2496 knock-out strain | |||||||||
Sample |
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Biological species | Treponema denticola (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Muok AR / Yang W / Briegel A | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Atypical chemoreceptor arrays accommodate high membrane curvature. Authors: Alise R Muok / Davi R Ortega / Kurni Kurniyati / Wen Yang / Zachary A Maschmann / Adam Sidi Mabrouk / Chunhao Li / Brian R Crane / Ariane Briegel / Abstract: The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended ...The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended array. Here, we report an alternative symmetry (P2) of the chemotaxis apparatus that emerges from a strict linear organization of the histidine kinase CheA in Treponema denticola cells, which possesses arrays with the highest native curvature investigated thus far. Using cryo-ET, we reveal that Td chemoreceptor arrays assume an unusual arrangement of the supra-molecular protein assembly that has likely evolved to accommodate the high membrane curvature. The arrays have several atypical features, such as an extended dimerization domain of CheA and a variant CheW-CheR-like fusion protein that is critical for maintaining an ordered chemosensory apparatus. Furthermore, the previously characterized Td oxygen sensor ODP influences CheA ordering. These results suggest a greater diversity of the chemotaxis signaling system than previously thought. | |||||||||
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_11384.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-11384-v30.xml emd-11384.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11384_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_11384.png | 31 KB | ||
Masks | emd_11384_msk_1.map | 8 MB | Mask map | |
Others | emd_11384_half_map_1.map.gz emd_11384_half_map_2.map.gz | 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11384 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11384 | HTTPS FTP |
-Validation report
Summary document | emd_11384_validation.pdf.gz | 339.8 KB | Display | EMDB validaton report |
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Full document | emd_11384_full_validation.pdf.gz | 339 KB | Display | |
Data in XML | emd_11384_validation.xml.gz | 10.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11384 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11384 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11384.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Treponema denticola arrays in an ODP (TDE2498) and TDE2496 knock-out strain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.026 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11384_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_11384_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_11384_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion...
Entire | Name: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant |
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Components |
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-Supramolecule #1: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion...
Supramolecule | Name: Chemotaxis arrays in a Treponema denticola ODP (TDE2498) deletion mutant type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Treponema denticola (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 20 K / Instrument: LEICA PLUNGER |
-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: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |