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- EMDB-42139: Cryo-EM structure of the flagellar MotAB stator bound to FliG -

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Basic information

Entry
Database: EMDB / ID: EMD-42139
TitleCryo-EM structure of the flagellar MotAB stator bound to FliG
Map dataGlobal B-factor sharpened map
Sample
  • Complex: MotAB stator complexed with FliG
    • Protein or peptide: OmpA family protein
    • Protein or peptide: Motility protein A
    • Protein or peptide: Flagellar motor switch protein FliG
  • Ligand: water
Keywordsflagella chemotaxis motility type III secretion system / MEMBRANE PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / proton transmembrane transport / chemotaxis / plasma membrane
Similarity search - Function
Motility protein A, N-terminal / Motility protein A N-terminal / Flagellar motor protein MotA, conserved site / Flagellar motor protein motA family signature. / : / 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 ...Motility protein A, N-terminal / Motility protein A N-terminal / Flagellar motor protein MotA, conserved site / Flagellar motor protein motA family signature. / : / 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 / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Motility protein A / OmpA family protein
Similarity search - Component
Biological speciesClostridium sporogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsDeme JC / Johnson S / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
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
DepositionSep 27, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42139.png

Downloads & links

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Map

FileDownload / File: emd_42139.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal B-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 448 pix.
= 310.464 Å		0.69 Å/pix.
x 448 pix.
= 310.464 Å		0.69 Å/pix.
x 448 pix.
= 310.464 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.0922303 - 4.6314716
Average (Standard dev.)0.0012883502 (±0.073125355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 310.46402 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42139_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_42139_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened with deepEMhancer

Fileemd_42139_additional_2.map
AnnotationSharpened with deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_42139_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_42139_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MotAB stator complexed with FliG

EntireName: MotAB stator complexed with FliG
Components
  • Complex: MotAB stator complexed with FliG
    • Protein or peptide: OmpA family protein
    • Protein or peptide: Motility protein A
    • Protein or peptide: Flagellar motor switch protein FliG
  • Ligand: water

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Supramolecule #1: MotAB stator complexed with FliG

SupramoleculeName: MotAB stator complexed with FliG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Clostridium sporogenes (bacteria)

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Macromolecule #1: OmpA family protein

MacromoleculeName: OmpA family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium sporogenes (bacteria)
Molecular weightTheoretical: 32.078861 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARRNKKGGG GDEIRGDEWL ATFSDTITLL LTFFILLYSF SSVDAQKFQQ VASAMQVAMT GQSGNTIVDY NLKNGDVPLV GETTKLGRE TGSDAKSDSK EVYNEVNKFV DKNNLKSSVE VKEDGRGVII QLRDNVLFEI GRADIKPQSK QIMDKINGLI A TLPNEVIV ...String:
MARRNKKGGG GDEIRGDEWL ATFSDTITLL LTFFILLYSF SSVDAQKFQQ VASAMQVAMT GQSGNTIVDY NLKNGDVPLV GETTKLGRE TGSDAKSDSK EVYNEVNKFV DKNNLKSSVE VKEDGRGVII QLRDNVLFEI GRADIKPQSK QIMDKINGLI A TLPNEVIV EGHTDNVPIK NEVYGSNWEL STARAVNVLR YFVETKKQNP VRFTAAGYGE YRPIAQNNSD VNKAKNRRVN IV IVSKEKE SSKKENLYFQ GQFGSWSHPQ FEKGGGSGGG SGGGSWSHPQ FEK

UniProtKB: OmpA family protein

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Macromolecule #2: Motility protein A

MacromoleculeName: Motility protein A / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Clostridium sporogenes (bacteria)
Molecular weightTheoretical: 28.92885 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRDILTPI GFVLCFGLVL WGMASGGSNL KVFWDVASVF ITIGGSMAAM LITYPMDEFK RLLIVIRQTF KDNGMSNIDV IQNFVDLSR KARREGLLSL EDAINNLTDD YMKKGLRMVV DGIEPETIRE IMELEIDEME KRHKSGADML KTWGGYAPAF G MVGTLIGL ...String:
MKKRDILTPI GFVLCFGLVL WGMASGGSNL KVFWDVASVF ITIGGSMAAM LITYPMDEFK RLLIVIRQTF KDNGMSNIDV IQNFVDLSR KARREGLLSL EDAINNLTDD YMKKGLRMVV DGIEPETIRE IMELEIDEME KRHKSGADML KTWGGYAPAF G MVGTLIGL IQMLANLTDS STIASGMGKA LITTFYGSLM ANAVFNPMGA NLMFKSGVEA TTREMVLEGV LAIQSGVNPR IM EEKLVSY LSPPERQAYS KVQVS

UniProtKB: Motility protein A

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Macromolecule #3: Flagellar motor switch protein FliG

MacromoleculeName: Flagellar motor switch protein FliG / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridium sporogenes (bacteria)
Molecular weightTheoretical: 11.311659 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GGGSGGGSGG GSVFEDIITL DDVAIQRVLR EVETKDLALA LKGSSEEVAN VIFRNQSKRA ASSLKEDIEF LGPVRIMDVE KAQQGIVSI IRRLDEAGEI VISRGGED

UniProtKB: Flagellar motor switch protein FliG

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 56.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 719539
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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