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- EMDB-60008: Structure of the RBM3 ring of Salmonella flagellar MS-ring protei... -

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Basic information

Entry
Database: EMDB / ID: EMD-60008
TitleStructure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied
Map data
Sample
  • Complex: Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied
    • Protein or peptide: Flagellar M-ring protein
KeywordsBacterial flagellum / flagellar assembly / electron Cryomicroscopy / MS-ring / type III secretion system / Salmonella / 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) / Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKinoshita M / Makino F / Miyata T / Imada K / Minamino T / Namba K
Funding support Japan, 10 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20K15749 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06162 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03182 Japan
Japan Society for the Promotion of Science (JSPS)JP22H02573 Japan
Japan Society for the Promotion of Science (JSPS)JP22K19274 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP20H05532 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H04844 Japan
CitationJournal: Commun Biol / Year: 2025
Title: Structural basis for assembly and function of the Salmonella flagellar MS-ring with three different symmetries.
Authors: Miki Kinoshita / Fumiaki Makino / Tomoko Miyata / Katsumi Imada / Keiichi Namba / Tohru Minamino /
Abstract: The flagellar MS-ring is the initial template for flagellar assembly and houses the flagellar protein export complex. The MS-ring has three parts of different symmetries within the ring structure by ...The flagellar MS-ring is the initial template for flagellar assembly and houses the flagellar protein export complex. The MS-ring has three parts of different symmetries within the ring structure by assembly of FliF subunits in two different conformations with distinct arrangements of three ring-building motifs, RBM1, RBM2, and RBM3. However, it remains unknown how these symmetries are generated. A combination of cryoEM structure and structure-based mutational analyses demonstrates that the well-conserved DQxGxxL motif in the RBM2-RBM3 hinge loop allows RBM2 to take two different orientations relative to RBM3. Of 34 FliF subunits of the MS-ring in the basal body, 23 RBM2 domains form an inner ring with a central pore that accommodates the flagellar protein export complex, and the remaining 11 RBM2 domains form 11 cog-like structures together with RBM1 domains just outside the inner RBM2-ring. We propose that a dimer of FliF with two different conformations initiates MS-ring assembly.
History
DepositionMay 3, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60008.png

Downloads & links

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Map

FileDownload / File: emd_60008.map.gz / Format: CCP4 / Size: 244.1 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 Å/pix.
x 400 pix.
= 400. Å		1 Å/pix.
x 400 pix.
= 400. Å		1 Å/pix.
x 400 pix.
= 400. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.126389 - 0.19363263
Average (Standard dev.)0.00014240133 (±0.005355693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60008_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_60008_half_map_2.map
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Sample components

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Entire : Structure of the RBM3 ring of Salmonella flagellar MS-ring protei...

EntireName: Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied
Components
  • Complex: Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied
    • Protein or peptide: Flagellar M-ring protein

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Supramolecule #1: Structure of the RBM3 ring of Salmonella flagellar MS-ring protei...

SupramoleculeName: Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied
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: 33 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 61.295645 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
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
50.0 mMNaClsodium chloride
25.0 mMImidazoleImidazole
50.0 mMTristris(hydroxymethyl)aminomethane
0.05 %LMNGLauryl maltose neopentyl glycol
0.05 %TritonTriton X-100
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4885 / Average electron dose: 40.0 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: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1015741
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 70250
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7d84

source_name: PDB, initial_model_type: experimental model7D84

7cik

source_name: PDB, initial_model_type: experimental model7CIK
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8zdt:
Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied

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