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Yorodumi- EMDB-8603: Sub-tomogram average of the archaellar motor in Thermococcus koda... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8603 | |||||||||
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Title | Sub-tomogram average of the archaellar motor in Thermococcus kodakaraensis | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Thermococcus kodakaraensis (archaea) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 40.0 Å | |||||||||
Authors | Chang Y-W / Kjaer A / Briegel A / Oikonomou CM / Jensen GJ | |||||||||
Citation | Journal: EMBO Rep / Year: 2017 Title: Morphology of the archaellar motor and associated cytoplasmic cone in . Authors: Ariane Briegel / Catherine M Oikonomou / Yi-Wei Chang / Andreas Kjær / Audrey N Huang / Ki Woo Kim / Debnath Ghosal / Hong H Nguyen / Dorothy Kenny / Rachel R Ogorzalek Loo / Robert P ...Authors: Ariane Briegel / Catherine M Oikonomou / Yi-Wei Chang / Andreas Kjær / Audrey N Huang / Ki Woo Kim / Debnath Ghosal / Hong H Nguyen / Dorothy Kenny / Rachel R Ogorzalek Loo / Robert P Gunsalus / Grant J Jensen / Abstract: Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a ...Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a peptidoglycan cell wall, is unknown. Here, we use electron cryotomography to visualize the archaellar basal body in KOD1. Compared to the homologous bacterial type IV pilus (T4P), we observe structural similarities as well as several unique features. While the position of the cytoplasmic ATPase appears conserved, it is not braced by linkages that extend upward through the cell envelope as in the T4P, but rather by cytoplasmic components that attach it to a large conical frustum up to 500 nm in diameter at its base. In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome-excluding material and may function as a polar organizing center for the coccoid cells. | |||||||||
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_8603.map.gz | 827.5 KB | EMDB map data format | |
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Header (meta data) | emd-8603-v30.xml emd-8603.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_8603.png | 52.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8603 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8603 | HTTPS FTP |
-Validation report
Summary document | emd_8603_validation.pdf.gz | 297.1 KB | Display | EMDB validaton report |
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Full document | emd_8603_full_validation.pdf.gz | 296.7 KB | Display | |
Data in XML | emd_8603_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_8603_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8603 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8603 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8603.map.gz / Format: CCP4 / Size: 977.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 6.6 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 : Archaellar motor
Entire | Name: Archaellar motor |
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Components |
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-Supramolecule #1: Archaellar motor
Supramolecule | Name: Archaellar motor / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermococcus kodakaraensis (archaea) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 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: Tecnai Polara / Image courtesy: FEI Company |