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- EMDB-42451: Cryo-EM structure of a Clockwise locked form of the Salmonella en... -

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Basic information

Entry
Database: EMDB / ID: EMD-42451
TitleCryo-EM structure of a Clockwise locked form of the Salmonella enterica Typhimurium flagellar C-ring, with C34 symmetry applied
Map dataClockwise locked form of the Salmonella enterica Typhimurium flagellar C-ring, with C34 symmetry applied
Sample
  • Complex: Intact C34 flagellar C-ring from purified basal bodies, clockwise locked.
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar motor switch protein FliGFlagellar motor switch protein
    • Protein or peptide: Flagellar motor switch protein FliMFlagellar motor switch protein
    • Protein or peptide: Flagellar motor switch protein FliNFlagellar motor switch protein
KeywordsFlagella / Salmonella / C-ring / motor / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / 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 FliG / Flagellar motor switch protein FliM / 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 ...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 FliG / Flagellar motor switch protein FliM / 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 / Flagellar motor switch protein FliM / FliG middle domain / FliG N-terminal domain / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / 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 M-ring protein / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsJohnson S / Deme JC / Lea SM
Funding support United States, United Kingdom, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Wellcome Trust201536 United Kingdom
Wellcome Trust219477 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: Nat Microbiol / Year: 2024
Title: Structural basis of directional switching by the bacterial flagellum.
Authors: Steven Johnson / Justin C Deme / Emily J Furlong / Joseph J E Caesar / Fabienne F V Chevance / Kelly T Hughes / Susan M Lea /
Abstract: The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar ...The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotAB stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.
History
DepositionOct 22, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42451.png

Downloads & links

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Map

FileDownload / File: emd_42451.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClockwise locked form of the Salmonella enterica Typhimurium flagellar C-ring, with C34 symmetry applied
Voxel sizeX=Y=Z: 1.664 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.26197243 - 1.2710295
Average (Standard dev.)0.0069049452 (±0.087832995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 851.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42451_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_42451_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_42451_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_42451_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Intact C34 flagellar C-ring from purified basal bodies, clockwise...

EntireName: Intact C34 flagellar C-ring from purified basal bodies, clockwise locked.
Components
  • Complex: Intact C34 flagellar C-ring from purified basal bodies, clockwise locked.
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar motor switch protein FliGFlagellar motor switch protein
    • Protein or peptide: Flagellar motor switch protein FliMFlagellar motor switch protein
    • Protein or peptide: Flagellar motor switch protein FliNFlagellar motor switch protein

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Supramolecule #1: Intact C34 flagellar C-ring from purified basal bodies, clockwise...

SupramoleculeName: Intact C34 flagellar C-ring from purified basal bodies, clockwise locked.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (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 subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 61.295645 KDa
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
Details: Residues 169-171 (PAA) were deleted on the chromosome.
Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 36.651688 KDa
SequenceString: MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ ...String:
MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ LAELTEVLNG LLDGQNLKRS KMGGVRTAAE IINLMKTQQE EAVITAVREF DGELAQKIID EMFLFENLVD VD DRSIQRL LQEVDSESLL IALKGAEPPL REKFLRNMSQ RAADILRDDL ANRGPVRLSQ VENEQKAILL IVRRLAETGE MVI GSGEDT YV

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: 37.901066 KDa
SequenceString: MGDSILSQAE IDALLNGDSD TKDEPTPGIA SDSDIRPYDP NTQRRVVRER LQALEIINER FARQFRMGLF NLLRRSPDIT VGAIRIQPY HEFARNLPVP TNLNLIHLKP LRGTGLVVFS PSLVFIAVDN LFGGDGRFPT KVEGREFTHT EQRVINRMLK L ALEGYSDA ...String:
MGDSILSQAE IDALLNGDSD TKDEPTPGIA SDSDIRPYDP NTQRRVVRER LQALEIINER FARQFRMGLF NLLRRSPDIT VGAIRIQPY HEFARNLPVP TNLNLIHLKP LRGTGLVVFS PSLVFIAVDN LFGGDGRFPT KVEGREFTHT EQRVINRMLK L ALEGYSDA WKAINPLEVE YVRSEMQVKF TNITTSPNDI VVNTPFHVEI GNLTGEFNIC LPFSMIEPLR ELLVNPPLEN SR HEDQNWR DNLVRQVQHS ELELVANFAD IPLRLSQILK LKPGDVLPIE KPDRIIAHVD GVPVLTSQYG TVNGQYALRV EHL INPILN SLNEEQPK

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
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: 8.5
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19363
FSC plot (resolution estimation)

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