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- EMDB-61731: Polyrod formed by FlgG (G65V) from the Salmonella TH26292 strain -

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Basic information

Entry
Database: EMDB / ID: EMD-61731
TitlePolyrod formed by FlgG (G65V) from the Salmonella TH26292 strain
Map data
Sample
  • Organelle or cellular component: Polyrod composed of FlgG(G65V)
    • Protein or peptide: Flagellar basal-body rod protein FlgG
Keywordsflagella motor. polyrod / P ring on polyrod complex / Cryo-EM / SPA / Salmonella / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar basal-body rod FlgG / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar basal-body rod protein FlgG
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 3.37 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: to be published
Title: Structural insights into the assembly mechanism of the molecular bushing of the bacterial flagellar motor
Authors: Yamaguchi T / Kato T / Minamino T / Namba K
History
DepositionSep 27, 2024-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61731.png

Downloads & links

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Map

FileDownload / File: emd_61731.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116
Minimum - Maximum-0.052354347 - 0.34676334
Average (Standard dev.)0.0045260834 (±0.024004646)
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_61731_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61731_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61731_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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)
    • Protein or peptide: Flagellar basal-body rod protein FlgG

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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: all
Details: Polyrod from the complex of P ring attached to polyrod. The FlgG(G65V) mutant of flagellar motor from Salmonella enterica serva typhimurium
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: Flagellar basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 1
Details: G65V is a natural mutation isolated from the engineered strain TH26292.
Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: TH26292
Molecular weightTheoretical: 27.826887 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
SequenceString: MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSVLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV ...String:
MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSVLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV QVGQLNLTTF MNDTGLESIG ENLYIETQSS GAPNESTPGL NGAGLLYQGY VETSNVNVAE ELVNMIQVQR AY EINSKAV STTDQMLQKL TQL

UniProtKB: Flagellar basal-body rod protein FlgG

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical 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
StainingType: NEGATIVE / Material: Uranyl acetate
Details: The condition and concentration of purified samples were checked before making cryoEM sample grid. A 3 microliter aliquot of the sample solutions was placed on a thin carbon-coated, 20 ...Details: The condition and concentration of purified samples were checked before making cryoEM sample grid. A 3 microliter aliquot of the sample solutions was placed on a thin carbon-coated, 20 seconds glow-discharged copper grid. The extra solution was removed from the grid by blotting, the filaments and cells were stained with 2% and 0.2% phosphotungstic acid (PTA), respectively, and the purified protein samples were stained with 2% uranyl acetate. The sample grids were dried for 1 hour at room temperature and checked using a transmission electron microscope, JEM-1011 (JEOL, Akishima, Japan) with an accelerating voltage of 100 kV.
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: NITROGEN / 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 / 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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.31 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 88969
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 386473 / Software - Name: cryoSPARC (ver. 3.2.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7cbm


Details: FlgG protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Final angle assignmentType: PROJECTION MATCHING

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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
Output model

PDB-9jqo:
Polyrod formed by FlgG (G65V) from the Salmonella TH26292 strain

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