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- EMDB-37590: Cryo-EM structure of the MS ring (C34) within the flagellar motor... -

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Basic information

Entry
Database: EMDB / ID: EMD-37590
TitleCryo-EM structure of the MS ring (C34) within the flagellar motor-hook complex in the CW state
Map dataExperimental map
Sample
  • Complex: C ring-containing flagellar motor-hook complex in the CW state
    • Protein or peptide: Flagellar M-ring protein
KeywordsFlagellum / Flagellar motor / MS ring / MOTOR 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTan JX / Zhang L / Zhou Y / Zhu YQ
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)U23A20163 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: Cell Res / Year: 2024
Title: Structural basis of the bacterial flagellar motor rotational switching.
Authors: Jiaxing Tan / Ling Zhang / Xingtong Zhou / Siyu Han / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the ...The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the switch complex for the rotational direction switching from counterclockwise to clockwise. However, the structural basis of the rotational switching and how the C ring is assembled have long remained elusive. Here, we present two high-resolution cryo-electron microscopy structures of the C ring-containing flagellar basal body-hook complex from Salmonella Typhimurium, which are in the default counterclockwise state and in a constitutively active CheY mutant-induced clockwise state, respectively. In both complexes, the C ring consists of four subrings, but is in two different conformations. The CheY proteins are bound into an open groove between two adjacent protomers on the surface of the middle subring of the C ring and interact with the FliG and FliM subunits. The binding of the CheY protein induces a significant upward shift of the C ring towards the MS ring and inward movements of its protomers towards the motor center, which eventually remodels the structures of the FliG subunits and reverses the orientations and surface electrostatic potential of the α helices to trigger the counterclockwise-to-clockwise rotational switching. The conformational changes of the FliG subunits reveal that the stator units on the motor require a relocation process in the inner membrane during the rotational switching. This study provides unprecedented molecular insights into the rotational switching mechanism and a detailed overall structural view of the bacterial flagellar motors.
History
DepositionSep 26, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37590.png

Downloads & links

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Map

FileDownload / File: emd_37590.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExperimental map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.5196455 - 3.463512
Average (Standard dev.)-0.0014775413 (±0.08181985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 614.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_37590_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_37590_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 : C ring-containing flagellar motor-hook complex in the CW state

EntireName: C ring-containing flagellar motor-hook complex in the CW state
Components
  • Complex: C ring-containing flagellar motor-hook complex in the CW state
    • Protein or peptide: Flagellar M-ring protein

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Supramolecule #1: C ring-containing flagellar motor-hook complex in the CW state

SupramoleculeName: C ring-containing flagellar motor-hook complex in the CW state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (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 str. LT2 (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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
11.7 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride
4.17 mMEDTAethylenediaminetetraacetic acid
0.083 % v/vTX-100octylphenol ethoxylate
25.0 mMNaClsodium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot time: 4 Blot force: 10 Wait time: 30 Blot total: 1 Drain time: 2.
DetailsThis sample was prepared by incubating the C ring-containing flagellar motor-hook complex with the constitutively active mutant of CheY (CheY**)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 46058 / Details: Particles were manually picked using cryoSPARC
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C34 (34 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 24190
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Model-Angelo
SoftwareName: UCSF Chimera (ver. 1.17)
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8wjr:
Cryo-EM structure of the MS ring (C34) within the flagellar motor-hook complex in the CW state

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