+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30613 | |||||||||||||||||||||||||||||||||||||||
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Title | Structure of the bacterial flagellar basal body | |||||||||||||||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||||||||||||||
Sample |
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Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Kawamoto A / Miyata T / Makino F / Kinoshita M / Minamino T / Imada K / Kato T / Namba K | |||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 12 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries. Authors: Akihiro Kawamoto / Tomoko Miyata / Fumiaki Makino / Miki Kinoshita / Tohru Minamino / Katsumi Imada / Takayuki Kato / Keiichi Namba / Abstract: The bacterial flagellar MS ring is a transmembrane complex acting as the core of the flagellar motor and template for flagellar assembly. The C ring attached to the MS ring is involved in torque ...The bacterial flagellar MS ring is a transmembrane complex acting as the core of the flagellar motor and template for flagellar assembly. The C ring attached to the MS ring is involved in torque generation and rotation switch, and a large symmetry mismatch between these two rings has been a long puzzle, especially with respect to their role in motor function. Here, using cryoEM structural analysis of the flagellar basal body and the MS ring formed by full-length FliF from Salmonella enterica, we show that the native MS ring is formed by 34 FliF subunits with no symmetry variation. Symmetry analysis of the C ring shows a variation with a peak at 34-fold, suggesting flexibility in C ring assembly. Finally, our data also indicate that FliF subunits assume two different conformations, contributing differentially to the inner and middle parts of the M ring and thus resulting in 23- and 11-fold subsymmetries in the inner and middle M ring, respectively. The internal core of the M ring, formed by 23 subunits, forms a hole of the right size to accommodate the protein export gate. | |||||||||||||||||||||||||||||||||||||||
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_30613.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-30613-v30.xml emd-30613.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30613_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_30613.png | 31.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30613 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30613 | HTTPS FTP |
-Validation report
Summary document | emd_30613_validation.pdf.gz | 359.2 KB | Display | EMDB validaton report |
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Full document | emd_30613_full_validation.pdf.gz | 358.7 KB | Display | |
Data in XML | emd_30613_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | emd_30613_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30613 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30613 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30613.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.8 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 : Flagellar basal body complex from Salmonella enterica serovar Typ...
Entire | Name: Flagellar basal body complex from Salmonella enterica serovar Typhimurium |
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Components |
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-Supramolecule #1: Flagellar basal body complex from Salmonella enterica serovar Typ...
Supramolecule | Name: Flagellar basal body complex from Salmonella enterica serovar Typhimurium type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Sugar embedding | Material: Buffer | ||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number real images: 18256 / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |