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- EMDB-43328: CW Flagellar Switch Complex with extra density - FliF, FliG, FliM... -

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Basic information

Entry
Database: EMDB / ID: EMD-43328
TitleCW Flagellar Switch Complex with extra density - FliF, FliG, FliM, and FliN forming the C-ring from Salmonella
Map dataMap built from applying symmetry to a locally refined region.
Sample
  • Complex: Flagellar C-ring containing FliF, FliG, FliM, and FliN
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar motor switch protein FliG
    • Protein or peptide: Flagellar motor switch protein FliM
    • Protein or peptide: Flagellar motor switch protein FliN
KeywordsDomain Swap / Symmetry mismatch / Flagellar component / Switch complex / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal ...Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / 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 motor switch protein FliG / Flagellar motor switch protein FliM / Flagellar M-ring protein / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsSingh PK / Iverson TM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)GM61606 United States
CitationJournal: Nat Microbiol / Year: 2024
Title: CryoEM structures reveal how the bacterial flagellum rotates and switches direction.
Authors: Prashant K Singh / Pankaj Sharma / Oshri Afanzar / Margo H Goldfarb / Elena Maklashina / Michael Eisenbach / Gary Cecchini / T M Iverson /
Abstract: Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural ...Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or 'switch', limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.
History
DepositionJan 9, 2024-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43328.png

Downloads & links

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Map

FileDownload / File: emd_43328.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap built from applying symmetry to a locally refined region.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 512 pix.
= 1047.04 Å		2.05 Å/pix.
x 512 pix.
= 1047.04 Å		2.05 Å/pix.
x 512 pix.
= 1047.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.060174905 - 0.28314713
Average (Standard dev.)-0.0011007149 (±0.018393435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1047.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Flagellar C-ring containing FliF, FliG, FliM, and FliN

EntireName: Flagellar C-ring containing FliF, FliG, FliM, and FliN
Components
  • Complex: Flagellar C-ring containing FliF, FliG, FliM, and FliN
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar motor switch protein FliG
    • Protein or peptide: Flagellar motor switch protein FliM
    • Protein or peptide: Flagellar motor switch protein FliN

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Supramolecule #1: Flagellar C-ring containing FliF, FliG, FliM, and FliN

SupramoleculeName: Flagellar C-ring containing FliF, FliG, FliM, and FliN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 3.5 MDa

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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 subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 61.295645 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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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Macromolecule #2: Flagellar motor switch protein FliG

MacromoleculeName: Flagellar motor switch protein FliG / type: protein_or_peptide / ID: 2 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 36.86093 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR GQAADILALF DERLRHDVML R IATFGGVQ ...String:
MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR GQAADILALF DERLRHDVML R IATFGGVQ PAALAELTEV LNGLLDGQNL KRSKMGGVRT AAEIINLMKT QQEEAVITAV REFDGELAQK IIDEMFLFEN LV DVDDRSI QRLLQEVDSE SLLIALKGAE PPLREKFLRN MSQRAADILR DDLANRGPVR LSQVENEQKA ILLIVRRLAE TGE MVIGSG EDTYV

UniProtKB: Flagellar motor switch protein FliG

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Macromolecule #3: Flagellar motor switch protein FliM

MacromoleculeName: Flagellar motor switch protein FliM / type: protein_or_peptide / ID: 3 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 32.992895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)LQA LEIINERFAR QFRMGLFNLL RRSPDITVGA IRIQPYHEFA RN LPVPTNL NLIHLKPLRG TGLVVFSPSL VFIAVDNLFG GDGRFPTKVE GREFTHTEQR VINRMLKLAL EGYSDAWKAI NPL EVEYVR ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)LQA LEIINERFAR QFRMGLFNLL RRSPDITVGA IRIQPYHEFA RN LPVPTNL NLIHLKPLRG TGLVVFSPSL VFIAVDNLFG GDGRFPTKVE GREFTHTEQR VINRMLKLAL EGYSDAWKAI NPL EVEYVR SEMQVKFTNI TTSPNDIVVN TPFHVEIGNL TGEFNICLPF SMIEPLRELL VNPPLENSRH EDQNWRDNLV RQVQ HSELE LVANFADIPL RLSQILKLKP GDVLPIEKPD RIIAHVDGVP VLTSQYGTVN GQYALRVEHL INPILNSLNE EQPK

UniProtKB: Flagellar motor switch protein FliM

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Macromolecule #4: Flagellar motor switch protein FliN

MacromoleculeName: Flagellar motor switch protein FliN / type: protein_or_peptide / ID: 4 / Number of copies: 102 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 14.801823 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSDMNNPSDE NTGALDDLWA DALNEQKATT TKSAADAVFQ QLGGGDVSGA MQDIDLIMDI PVKLTVELGR TRMTIKELLR LTQGSVVAL DGLAGEPLDI LINGYLIAQG EVVVVADKYG VRITDIITPS ERMRRLSR

UniProtKB: Flagellar motor switch protein FliN

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.242 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
cryoSPARC (ver. 4.2.1)
RELION (ver. 4.0.1)region_image_handler to apply C34 symmetry to build the ring

Number images used: 11106
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)

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