+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30612 | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 34-fold symmetry Salmonella S ring formed by full-length FliF | ||||||||||||||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||||||||||||||
Keywords | Flagellar motor / Type III protein export system / Transmembrane protein Complex / Torque generation / MEMBRANE PROTEIN | ||||||||||||||||||||||||||||||||||||
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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) / Salmonella enterica serovar Typhimurium (bacteria) | ||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||||||||||||||||||||
Authors | Kawamoto A / Miyata T | ||||||||||||||||||||||||||||||||||||
Funding support | Japan, 11 items
| ||||||||||||||||||||||||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30612.map.gz | 289.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30612-v30.xml emd-30612.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
Images | emd_30612.png | 178.6 KB | ||
Masks | emd_30612_msk_1.map | 307.5 MB | Mask map | |
Filedesc metadata | emd-30612.cif.gz | 6.2 KB | ||
Others | emd_30612_half_map_1.map.gz emd_30612_half_map_2.map.gz | 284.8 MB 284.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30612 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30612 | HTTPS FTP |
-Validation report
Summary document | emd_30612_validation.pdf.gz | 846.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30612_full_validation.pdf.gz | 845.8 KB | Display | |
Data in XML | emd_30612_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_30612_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30612 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30612 | HTTPS FTP |
-Related structure data
Related structure data | 7d84MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30612.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_30612_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_30612_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_30612_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : transmembrane protein complex made of FliF
Entire | Name: transmembrane protein complex made of FliF |
---|---|
Components |
|
-Supramolecule #1: transmembrane protein complex made of FliF
Supramolecule | Name: transmembrane protein complex made of FliF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: the MS ring formed by full-length FliF from Salmonella enterica serovar Typhimurium |
---|---|
Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
-Macromolecule #1: Flagellar M-ring protein
Macromolecule | Name: Flagellar M-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 34 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Salmonella enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 61.295645 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE ...String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE QKSPSASVTV TLEPGRALDE GQISAVVHLV SSAVAGLPPG NVTLVDQSGH LLTQSNTSGR DLNDAQLKFA ND VESRIQR RIEAILSPIV GNGNVHAQVT AQLDFANKEQ TEEHYSPNGD ASKATLRSRQ LNISEQVGAG YPGGVPGALS NQP APPNEA PIATPPTNQQ NAQNTPQTST STNSNSAGPR STQRNETSNY EVDRTIRHTK MNVGDIERLS VAVVVNYKTL ADGK PLPLT ADQMKQIEDL TREAMGFSDK RGDTLNVVNS PFSAVDNTGG ELPFWQQQSF IDQLLAAGRW LLVLVVAWIL WRKAV RPQL TRRVEEAKAA QEQAQVRQET EEAVEVRLSK DEQLQQRRAN QRLGAEVMSQ RIREMSDNDP RVVALVIRQW MSNDHE UniProtKB: Flagellar M-ring protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. | ||||||||||
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) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-6 / Number grids imaged: 1 / Number real images: 1589 / 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|---|
Output model | PDB-7d84: |