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- EMDB-80383: Polyrod without P-ring formed by FlgG (G65V) from the Salmonella ... -

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Basic information

Entry
Database: EMDB / ID: EMD-80383
TitlePolyrod without P-ring formed by FlgG (G65V) from the Salmonella TH26292 strain
Map data
Sample
  • Organelle or cellular component: Polyrod composed of FlgG(G65V)
Keywordsflagella motor. polyrod / P ring on polyrod complex / Cryo-EM / SPA / Salmonella / MOTOR PROTEIN
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsYamaguchi T / Kato T / Minamino T / Namba K
Funding support Japan, 9 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP25000013MEXT KAKENHI Grant Number JP15H01640,JP20H05532 Japan
Japan Society for the Promotion of Science (JSPS)JP18K06155 Japan
Japan Society for the Promotion of Science (JSPS)JP26293097 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03182 Japan
Japan Society for the Promotion of Science (JSPS)JP15H01640 Japan
Japan Society for the Promotion of Science (JSPS)Japan Society for the Promotion of Science (JSPS) Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Society for the Promotion of Science (JSPS)JP21J12128 Japan
CitationJournal: Commun Biol / Year: 2026
Title: Structural insights into the assembly mechanism of the molecular bushing in the bacterial flagellar motor.
Authors: Tomoko Yamaguchi / Tohru Minamino / Takayuki Kato / Fabienne F V Chevance / Kelly T Hughes / Keiichi Namba /
Abstract: The LP-ring complex of the Salmonella flagellar motor acts as a bushing that supports high-speed rotation of the rod, which serves as a drive shaft. The L-ring, P-ring, and distal rod consist of ...The LP-ring complex of the Salmonella flagellar motor acts as a bushing that supports high-speed rotation of the rod, which serves as a drive shaft. The L-ring, P-ring, and distal rod consist of FlgH, FlgI, and FlgG, respectively. LP-ring formation begins with P-ring assembly around the distal rod, where it remains firmly attached until the L-ring assembles above it. L-ring formation induces P-ring detachment, allowing the rod to freely rotate within the LP-ring, but this mechanism remains unclear. Here, we report the cryoEM structure of the P-ring assembled on a polyrod, an unusually elongated rod structure. The P-ring exhibits a slightly elliptical shape with a 2.7° tilt relative to the rod axis for its stable attachment. However, L-ring assembly on the P-ring causes steric clashes with the rod to induce P-ring detachment, allowing it to adopt a circular shape and complete the LP-ring as a functional bushing.
History
DepositionApr 18, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_80383.png

Downloads & links

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Map

FileDownload / File: emd_80383.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 400 pix.
= 396. Å		0.99 Å/pix.
x 400 pix.
= 396. Å		0.99 Å/pix.
x 400 pix.
= 396. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.186
Minimum - Maximum-0.9363454 - 1.5944505
Average (Standard dev.)0.0029985069 (±0.057944182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80383_msk_1.map
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Additional map: #1

Fileemd_80383_additional_1.map
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Half map: #1

Fileemd_80383_half_map_1.map
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Half map: #2

Fileemd_80383_half_map_2.map
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Sample components

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Entire : Polyrod composed of FlgG(G65V)

EntireName: Polyrod composed of FlgG(G65V)
Components
  • Organelle or cellular component: Polyrod composed of FlgG(G65V)

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Supramolecule #1: Polyrod composed of FlgG(G65V)

SupramoleculeName: Polyrod composed of FlgG(G65V) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Polyrod isolated from the FlgG (G65V) mutant of the flagellar motor in Salmonella enterica serovar typhimurium
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 380 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HCltris(hydroxymethyl)aminomethane
50.0 mMNaClsodium Chloride
25.0 mMImidazoleImidazole
0.002 %LMNGLauryl Maltose Neopentyl Glycol
0.05 %TritonTriton X-100

Details: 50 mM Tris-HCl, 50 mM NaCl, 25 mM Imidazole, 0.002% (w/v) LMNG, 0.05% (w/v) Triton X-100, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blotting time of 4 seconds, 1 seconds drain time, force 0.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 28712 / Average exposure time: 6.0 sec. / Average electron dose: 75.0 e/Å2
Details: Using a minimum dose system, two data sets were taken by different conditions; One date set was taken by exposure of 6 seconds, a frame rate of 0.08 sec/frame, an electron dose of 1.0 ...Details: Using a minimum dose system, two data sets were taken by different conditions; One date set was taken by exposure of 6 seconds, a frame rate of 0.08 sec/frame, an electron dose of 1.0 electrons/A^2 per frame. The other was taken by exposure of 2.5 seconds, a frame rate of 0.0625 sec/frame, an electron dose of 1.0 electrons/A^2 per frame.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 0.2 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 50000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 304533
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 145980
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 3.2.0)

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Atomic model buiding 1

Initial modelPDB ID:

7cbm


Chain - Chain ID: B / Chain - Residue range: 1-260 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model consisted of the whole sequence of wild type FlgG
DetailsPhenix1.21-rc1 , refmac servalcat and ISOLDE was used for fitting, and Phenix was used for final fitting.
RefinementSpace: REAL / Protocol: OTHER

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