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Yorodumi- EMDB-30940: Salmonella flagella MS-ring protein FliF 1-503 having C33 symmetry -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30940 | ||||||||||||||||||||||||||||||||||||||||||
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Title | Salmonella flagella MS-ring protein FliF 1-503 having C33 symmetry | ||||||||||||||||||||||||||||||||||||||||||
Map data | FliF1-503 ring structure having 33 symmetry | ||||||||||||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information bacterial-type flagellum basal body, MS ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Makino F / Kawamoto A / Namba K | ||||||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 13 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_30940.map.gz | 39.5 MB | EMDB map data format | |
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Header (meta data) | emd-30940-v30.xml emd-30940.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_30940.png | 32.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30940 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30940 | HTTPS FTP |
-Validation report
Summary document | emd_30940_validation.pdf.gz | 390.8 KB | Display | EMDB validaton report |
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Full document | emd_30940_full_validation.pdf.gz | 390.4 KB | Display | |
Data in XML | emd_30940_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_30940_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30940 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30940 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30940.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | FliF1-503 ring structure having 33 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2 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 : Salmonella flagella MS-ring protein FliF 1-503
Entire | Name: Salmonella flagella MS-ring protein FliF 1-503 |
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Components |
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-Supramolecule #1: Salmonella flagella MS-ring protein FliF 1-503
Supramolecule | Name: Salmonella flagella MS-ring protein FliF 1-503 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 4.0 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 6566 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 40.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 0.4 µm / Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |