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- EMDB-62211: Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring... -

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Entry
Database: EMDB / ID: EMD-62211
TitleStructure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
Map data
Sample
  • Complex: Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
KeywordsBacterial flagellum / flagellar assembly / electron Cryomicroscopy / MS-ring / type III secretion system / Salmonella / MOTOR PROTEIN
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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
DepositionOct 29, 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

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emd_62211.png

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Map

FileDownload / File: emd_62211.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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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

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Voxel sizeX=Y=Z: 1 Å
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Contour LevelBy AUTHOR: 0.0123
Minimum - Maximum-0.006327788 - 0.03431792
Average (Standard dev.)0.00019038554 (±0.0021916337)
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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Mask #1

Fileemd_62211_msk_1.map
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Half map: #1

Fileemd_62211_half_map_1.map
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Half map: #2

Fileemd_62211_half_map_2.map
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Sample components

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Entire : Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring...

EntireName: Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
Components
  • Complex: Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied

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Supramolecule #1: Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring...

SupramoleculeName: Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)

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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
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: 4.2 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 modelPDB ID:

7d84


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: 7D84
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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