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- EMDB-37618: Cryo-EM structure of the LP ring within the flagellar motor-hook ... -

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Basic information

Entry
Database: EMDB / ID: EMD-37618
TitleCryo-EM structure of the LP ring within the flagellar motor-hook complex in the CCW state.
Map dataExperimental map
Sample
  • Complex: C ring-containing flagellar motor-hook complex in the CCW state
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
KeywordsFlagellum / Flagellar motor / LP ring / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Flagellar L-ring protein / Flagellar P-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 29, 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_37618.png

Downloads & links

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Map

FileDownload / File: emd_37618.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.)
1.33 Å/pix.
x 512 pix.
= 681.984 Å		1.33 Å/pix.
x 512 pix.
= 681.984 Å		1.33 Å/pix.
x 512 pix.
= 681.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-5.415996 - 5.866306
Average (Standard dev.)-0.003844901 (±0.19107969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 681.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_37618_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_37618_half_map_2.map
AnnotationHalf map B
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 CCW state

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

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

SupramoleculeName: C ring-containing flagellar motor-hook complex in the CCW 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 L-ring protein

MacromoleculeName: Flagellar L-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 24.726666 KDa
SequenceString: MQKYALHAYP VMALMVATLT GCAWIPAKPL VQGATTAQPI PGPVPVANGS IFQSAQPINY GYQPLFEDRR PRNIGDTLTI VLQENVSAS KSSSANASRD GKTSFGFDTV PRYLQGLFGN SRADMEASGG NSFNGKGGAN ASNTFSGTLT VTVDQVLANG N LHVVGEKQ ...String:
MQKYALHAYP VMALMVATLT GCAWIPAKPL VQGATTAQPI PGPVPVANGS IFQSAQPINY GYQPLFEDRR PRNIGDTLTI VLQENVSAS KSSSANASRD GKTSFGFDTV PRYLQGLFGN SRADMEASGG NSFNGKGGAN ASNTFSGTLT VTVDQVLANG N LHVVGEKQ IAINQGTEFI RFSGVVNPRT ISGSNSVPST QVADARIEYV GNGYINEAQN MGWLQRFFLN LSPM

UniProtKB: Flagellar L-ring protein

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Macromolecule #2: Flagellar P-ring protein

MacromoleculeName: Flagellar P-ring protein / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 38.194176 KDa
SequenceString: MFKALAGIVL ALVATLAHAE RIRDLTSVQG VRENSLIGYG LVVGLDGTGD QTTQTPFTTQ TLNNMLSQLG ITVPTGTNMQ LKNVAAVMV TASYPPFARQ GQTIDVVVSS MGNAKSLRGG TLLMTPLKGV DSQVYALAQG NILVGGAGAS AGGSSVQVNQ L NGGRITNG ...String:
MFKALAGIVL ALVATLAHAE RIRDLTSVQG VRENSLIGYG LVVGLDGTGD QTTQTPFTTQ TLNNMLSQLG ITVPTGTNMQ LKNVAAVMV TASYPPFARQ GQTIDVVVSS MGNAKSLRGG TLLMTPLKGV DSQVYALAQG NILVGGAGAS AGGSSVQVNQ L NGGRITNG AIIERELPTQ FGAGNTINLQ LNDEDFTMAQ QITDAINRAR GYGSATALDA RTVQVRVPSG NSSQVRFLAD IQ NMEVNVT PQDAKVVINS RTGSVVMNRE VTLDSCAVAQ GNLSVTVNRQ LNVNQPNTPF GGGQTVVTPQ TQIDLRQSGG SLQ SVRSSA NLNSVVRALN ALGATPMDLM SILQSMQSAG CLRAKLEII

UniProtKB: Flagellar P-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
10.0 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride
5.0 mMEDTAethylenediaminetetraacetic acid
0.1 %TX-100octylphenol ethoxylate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot time: 2 Blot force: -15 Wait time: 60 Blot total: 1.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22192 / Details: Particles were manually picked using cryoSPARC
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C26 (26 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 11858
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7cbl


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8wle:
Cryo-EM structure of the LP ring within the flagellar motor-hook complex in the CCW state.

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