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- PDB-8z4d: Structure of the S-ring region of the Vibrio flagellar MS-ring pr... -

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Basic information

Entry
Database: PDB / ID: 8z4d
TitleStructure of the S-ring region of the Vibrio flagellar MS-ring protein FliF with 34-fold symmetry applied
ComponentsFlagellar M-ring protein,Flagellar motor switch protein FliG
KeywordsMOTOR PROTEIN / Complex / Rotor
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 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 / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal ...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 / 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
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsTakekawa, N. / Nishikino, T. / Kishikawa, J. / Hirose, M. / Kato, T. / Imada, K. / Homma, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H00393 Japan
Japan Society for the Promotion of Science (JSPS)21H01772 Japan
Japan Society for the Promotion of Science (JSPS)22K18943 Japan
Japan Society for the Promotion of Science (JSPS)20H03220 Japan
CitationJournal: mBio / Year: 2024
Title: Structural analysis of S-ring composed of FliFG fusion proteins in marine polar flagellar motor.
Authors: Norihiro Takekawa / Tatsuro Nishikino / Jun-Ichi Kishikawa / Mika Hirose / Miki Kinoshita / Seiji Kojima / Tohru Minamino / Takayuki Uchihashi / Takayuki Kato / Katsumi Imada / Michio Homma /
Abstract: The marine bacterium possesses a polar flagellum driven by a sodium ion flow. The main components of the flagellar motor are the stator and rotor. The C-ring and MS-ring, which are composed of FliG ...The marine bacterium possesses a polar flagellum driven by a sodium ion flow. The main components of the flagellar motor are the stator and rotor. The C-ring and MS-ring, which are composed of FliG and FliF, respectively, are parts of the rotor. Here, we purified an MS-ring composed of FliF-FliG fusion proteins and solved the near-atomic resolution structure of the S-ring-the upper part of the MS-ring-using cryo-electron microscopy. This is the first report of an S-ring structure from , whereas, previously, only those from have been reported. The S-ring structure reveals novel features compared with that of , such as tilt angle differences of the RBM3 domain and the β-collar region, which contribute to the vertical arrangement of the upper part of the β-collar region despite the diversity in the RBM3 domain angles. Additionally, there is a decrease of the inter-subunit interaction between RBM3 domains, which influences the efficiency of the MS-ring formation in different bacterial species. Furthermore, although the inner-surface electrostatic properties of and S-rings are altered, the residues potentially interacting with other flagellar components, such as FliE and FlgB, are well structurally conserved in the S-ring. These comparisons clarified the conserved and non-conserved structural features of the MS-ring across different species.IMPORTANCEUnderstanding the structure and function of the flagellar motor in bacterial species is essential for uncovering the mechanisms underlying bacterial motility and pathogenesis. Our study revealed the structure of the S-ring, a part of its polar flagellar motor, and highlighted its unique features compared with the well-studied S-ring. The observed differences in the inter-subunit interactions and in the tilt angles between the and S-rings highlighted the species-specific variations and the mechanism for the optimization of MS-ring formation in the flagellar assembly. By concentrating on the region where the S-ring and the rod proteins interact, we uncovered conserved residues essential for the interaction. Our research contributes to the advancement of bacterial flagellar biology.
History
DepositionApr 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Flagellar M-ring protein,Flagellar motor switch protein FliG
2: Flagellar M-ring protein,Flagellar motor switch protein FliG
3: Flagellar M-ring protein,Flagellar motor switch protein FliG
4: Flagellar M-ring protein,Flagellar motor switch protein FliG
5: Flagellar M-ring protein,Flagellar motor switch protein FliG
6: Flagellar M-ring protein,Flagellar motor switch protein FliG
7: Flagellar M-ring protein,Flagellar motor switch protein FliG
8: Flagellar M-ring protein,Flagellar motor switch protein FliG
9: Flagellar M-ring protein,Flagellar motor switch protein FliG
A: Flagellar M-ring protein,Flagellar motor switch protein FliG
B: Flagellar M-ring protein,Flagellar motor switch protein FliG
C: Flagellar M-ring protein,Flagellar motor switch protein FliG
D: Flagellar M-ring protein,Flagellar motor switch protein FliG
E: Flagellar M-ring protein,Flagellar motor switch protein FliG
F: Flagellar M-ring protein,Flagellar motor switch protein FliG
G: Flagellar M-ring protein,Flagellar motor switch protein FliG
H: Flagellar M-ring protein,Flagellar motor switch protein FliG
I: Flagellar M-ring protein,Flagellar motor switch protein FliG
J: Flagellar M-ring protein,Flagellar motor switch protein FliG
K: Flagellar M-ring protein,Flagellar motor switch protein FliG
L: Flagellar M-ring protein,Flagellar motor switch protein FliG
M: Flagellar M-ring protein,Flagellar motor switch protein FliG
N: Flagellar M-ring protein,Flagellar motor switch protein FliG
O: Flagellar M-ring protein,Flagellar motor switch protein FliG
P: Flagellar M-ring protein,Flagellar motor switch protein FliG
Q: Flagellar M-ring protein,Flagellar motor switch protein FliG
R: Flagellar M-ring protein,Flagellar motor switch protein FliG
S: Flagellar M-ring protein,Flagellar motor switch protein FliG
T: Flagellar M-ring protein,Flagellar motor switch protein FliG
U: Flagellar M-ring protein,Flagellar motor switch protein FliG
V: Flagellar M-ring protein,Flagellar motor switch protein FliG
W: Flagellar M-ring protein,Flagellar motor switch protein FliG
X: Flagellar M-ring protein,Flagellar motor switch protein FliG
Y: Flagellar M-ring protein,Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)3,550,17234
Polymers3,550,17234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Flagellar M-ring protein,Flagellar motor switch protein FliG


Mass: 104416.828 Da / Num. of mol.: 34 / Mutation: G214S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Strain: 138-2 / Gene: fliF, Vag1382_20710, fliG, AL468_14360, JOS67_04865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q75N27, UniProt: A0A0T7EAG0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homomeric 34mer of FliFG fusion protein of Vibrio alginolyticus
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 104 kDa/nm / Experimental value: NO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: 138-2
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClC4H11NO31
2100 mMpotassium chlorideKCl1
30.0025 %(w/v)LMNGC47H88O221
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.3 sec. / Electron dose: 49.7 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 6372
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2059366
SymmetryPoint symmetry: C34 (34 fold cyclic)
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43546 / Symmetry type: POINT

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