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- EMDB-30612: 34-fold symmetry Salmonella S ring formed by full-length FliF -

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Basic information

Entry
Database: EMDB / ID: EMD-30612
Title34-fold symmetry Salmonella S ring formed by full-length FliF
Map data
Sample
  • Complex: transmembrane protein complex made of FliFTransmembrane protein
    • Protein or peptide: Flagellar M-ring protein
KeywordsFlagellar 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
Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar M-ring protein
Similarity search - Component
Biological speciesSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) / Salmonella enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKawamoto A / Miyata T
Funding support Japan, 11 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25000013 Japan
Japan Society for the Promotion of Science (JSPS)18K06155 Japan
Japan Society for the Promotion of Science (JSPS)18K14639 Japan
Japan Society for the Promotion of Science (JSPS)19H03182 Japan
Japan Society for the Promotion of Science (JSPS)26293097 Japan
Japan Society for the Promotion of Science (JSPS)15H05593 Japan
Japan Society for the Promotion of Science (JSPS)20K15749 Japan
Japan Society for the Promotion of Science (JSPS)15H02386 Japan
Japan Society for the Promotion of Science (JSPS)15H01640 Japan
Japan Agency for Medical Research and Development (AMED)19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)17pc0101020 Japan
CitationJournal: 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
DepositionOct 7, 2020-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.749
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.749
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d84
  • Surface level: 0.749
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7d84
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30612.png

Downloads & links

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Map

FileDownload / File: emd_30612.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.749 / Movie #1: 0.749
Minimum - Maximum-2.4688787 - 4.2294064
Average (Standard dev.)-0.004350459 (±0.0931004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 462.24002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z462.240462.240462.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-2.4694.229-0.004

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Supplemental data

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Mask #1

Fileemd_30612_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30612_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30612_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : transmembrane protein complex made of FliF

EntireName: transmembrane protein complex made of FliFTransmembrane protein
Components
  • Complex: transmembrane protein complex made of FliFTransmembrane protein
    • Protein or peptide: Flagellar M-ring protein

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Supramolecule #1: transmembrane protein complex made of FliF

SupramoleculeName: 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)

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Macromolecule #1: Flagellar M-ring protein

MacromoleculeName: 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 weightTheoretical: 61.295645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormula
25.0 mMTris-HClTris
1.0 mMEDTAEthylenediaminetetraacetic acid
50.0 mMNaClSodium chloride
0.05 %LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 339861
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 2.1), RELION (ver. 3.0))
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 2.14)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.14)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C34 (34 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 38889

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7d84:
34-fold symmetry Salmonella S ring formed by full-length FliF

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