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- EMDB-39763: Structure of the S-ring region of the Vibrio flagellar MS-ring pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-39763
TitleStructure of the S-ring region of the Vibrio flagellar MS-ring protein FliF with 35-fold symmetry applied
Map data
Sample
  • Complex: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
    • Protein or peptide: Flagellar M-ring protein,Flagellar motor switch protein FliG
KeywordsComplex / Rotor / MOTOR PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsTakekawa N / Nishikino T / Kishikawa J / Hirose M / Kato T / Imada K / Homma M
Funding support Japan, 4 items
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, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39763.png

Downloads & links

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Map

FileDownload / File: emd_39763.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 600 pix.
= 684. Å		1.14 Å/pix.
x 600 pix.
= 684. Å		1.14 Å/pix.
x 600 pix.
= 684. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-0.9662315 - 1.681908
Average (Standard dev.)-0.0005051296 (±0.036685105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 684.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39763_msk_1.map
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Half map: #1

Fileemd_39763_half_map_1.map
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Half map: #2

Fileemd_39763_half_map_2.map
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Sample components

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Entire : Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus

EntireName: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
Components
  • Complex: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
    • Protein or peptide: Flagellar M-ring protein,Flagellar motor switch protein FliG

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Supramolecule #1: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus

SupramoleculeName: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: 138-2
Molecular weightTheoretical: 104 kDa/nm

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

MacromoleculeName: Flagellar M-ring protein,Flagellar motor switch protein FliG
type: protein_or_peptide / ID: 1 / Number of copies: 35 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 104.416828 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNHKVHHHHH HIEGRHMADK STDLTVTEGG SDGALVASSD VDVESQNPDL EERSASKFDM AVGDLDLLRQ VVLVLSISIC VALIVMLFF WVKEPEMRPL GAYETEELIP VLDYLDQQKI NYKLDGNTIS VESSEYNSIK LGMVRSGVNQ ATEAGDDILL Q DMGFGVSQ ...String:
MNHKVHHHHH HIEGRHMADK STDLTVTEGG SDGALVASSD VDVESQNPDL EERSASKFDM AVGDLDLLRQ VVLVLSISIC VALIVMLFF WVKEPEMRPL GAYETEELIP VLDYLDQQKI NYKLDGNTIS VESSEYNSIK LGMVRSGVNQ ATEAGDDILL Q DMGFGVSQ RLEQERLKLS RERQLAQAIE EMKQVRKARV LLALPKHSVF VRHNQEASAS VFLTLSTGTN LKQQEVDSIV DM VASAVPG MKTSRITVTD QHGRLLSSGS QDPASAARRK EQELERSQEQ ALREKIDSVL LPILGYGNYT AQVDIQMDFS AVE QTRKRF DPNTPATRSE YALEDYNNGN MVAGIPGALS NQPPADASIP QDVAQMKDGS VMGQGSVRKE STRNFELDTT ISHE RKQTG TVARQTVSVA IKDRRQVNPD TGEVTYTPMS ESEINAIRQV LIGTVGFDQG RGDLLNVLSV KFAEPEAEQL EEPPI WEHP NFSDWVRWFA SALVIIVVVL VLVRPAMKKL LNPTSDDEDE MYGPDGLPIG ADGETSLIGS DIESSELFEF GSSIDL PNL HKDEDVLKAV RALVANEPEL AAQVVKNWMN DMANDIVPQD DNAAGMPVEL DVSTITGEEK AAILLLSLNE QDAAGII RH LEPKQVQRVG SAMAKAKDLS QDKVSAVHRA FLEDIQKYTN IGMGSEDFMR NALVAALGED KANNLVDQIL LGTGSKGL D SLKWMDPRQV ASIIVNEHPQ IQTIVLSYLE ADQSAEILSQ FPERVRLDLM MRIANLEEVQ PSALAELNEI MEKQFAGQA GAQAAKISGL KAAAEIMNYL DNNVEGLLME QIRDQDEDMA TQIQDLMFVF ENLVEVDDQG IQKLLRDVPQ DVLQKALKGA DDSLREKVF KNMSKRAAEM MRDDIEAMPP VRVADVEAAQ KEILAIARRM ADAGELMLSG GADEFL

UniProtKB: Flagellar M-ring protein, Flagellar motor switch protein FliG

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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
20.0 mMC4H11NO3Tris-HCl
100.0 mMKClpotassium chloride
0.0025 %(w/v)C47H88O22LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 6372 / Average exposure time: 7.3 sec. / Average electron dose: 49.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2059366
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C35 (35 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 184915
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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