+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30378 | |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Salmonella FliF-FliG ring complex | |||||||||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||||||||
Sample |
| |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, MS ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.6 Å | |||||||||||||||||||||||||||||||||
Authors | Kawamoto A / Kato T / Kinoshita M / Minamino T / Namba K | |||||||||||||||||||||||||||||||||
Funding support | Japan, 10 items
| |||||||||||||||||||||||||||||||||
Citation | Journal: mBio / Year: 2021 Title: Two Distinct Conformations in 34 FliF Subunits Generate Three Different Symmetries within the Flagellar MS-Ring. Authors: Norihiro Takekawa / Akihiro Kawamoto / Mayuko Sakuma / Takayuki Kato / Seiji Kojima / Miki Kinoshita / Tohru Minamino / Keiichi Namba / Michio Homma / Katsumi Imada / Abstract: The bacterial flagellum is a protein nanomachine essential for bacterial motility. The flagellar basal body contains several ring structures. The MS-ring is embedded in the cytoplasmic membrane and ...The bacterial flagellum is a protein nanomachine essential for bacterial motility. The flagellar basal body contains several ring structures. The MS-ring is embedded in the cytoplasmic membrane and is formed at the earliest stage of flagellar formation to serve as the base for flagellar assembly as well as a housing for the flagellar protein export gate complex. The MS-ring is formed by FliF, which has two transmembrane helices and a large periplasmic region. A recent electron cryomicroscopy (cryoEM) study of the MS-ring formed by overexpressed FliF revealed a symmetry mismatch between the S-ring and inner part of the M-ring. However, the actual symmetry relation in the native MS-ring and positions of missing domains remain obscure. Here, we show the structure of the M-ring by combining cryoEM and X-ray crystallography. The crystal structure of the N-terminal half of the periplasmic region of FliF showed that it consists of two domains (D1 and D2) resembling PrgK D1/PrgH D2 and PrgK D2/PrgH D3 of the injectisome. CryoEM analysis revealed that the inner part of the M-ring shows a gear wheel-like density with the inner ring of C23 symmetry surrounded by cogs with C11 symmetry, to which 34 copies of FliF fitted well. We propose that FliF adopts two distinct orientations in the M-ring relative to the rest of FliF, with 23 chains forming the wheel and 11 chains forming the cogs, and the 34 chains come together to form the S-ring with C34 symmetry for multiple functions of the MS-ring. The bacterial flagellum is a motility organelle formed by tens of thousands of protein molecules. At the earliest stage of flagellar assembly, a transmembrane protein, FliF, forms the MS-ring in the cytoplasmic membrane as the base for flagellar assembly. Here, we solved the crystal structure of a FliF fragment. Electron cryomicroscopy (cryoEM) structural analysis of the MS-ring showed that the M-ring and S-ring have different rotational symmetries. By docking the crystal structure of the FliF fragment into the cryoEM density map of the entire MS-ring, we built a model of the whole periplasmic region of FliF and proposed that FliF adopts two distinct conformations to generate three distinct C11, C23, and C34 symmetries within the MS-ring for its multiple functions. | |||||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30378.map.gz | 42.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30378-v30.xml emd-30378.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_30378.png | 65.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30378 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30378 | HTTPS FTP |
-Validation report
Summary document | emd_30378_validation.pdf.gz | 315.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30378_full_validation.pdf.gz | 314.7 KB | Display | |
Data in XML | emd_30378_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_30378_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30378 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30378 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30378.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Salmonella FliF-FliG ring complex
Entire | Name: Salmonella FliF-FliG ring complex |
---|---|
Components |
|
-Supramolecule #1: Salmonella FliF-FliG ring complex
Supramolecule | Name: Salmonella FliF-FliG ring complex / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |