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- EMDB-61835: Polyrod-P ring complex from Salmonella TH26292 strain -

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Basic information

Entry
Database: EMDB / ID: EMD-61835
TitlePolyrod-P ring complex from Salmonella TH26292 strain
Map data
Sample
  • Complex: Polyrod-P ring complex from Salmonella enterica subsp. enterica serovar Typhimurium HK26292 mutant
Keywordsflagella motor. P ring-polyrod complex / Cryo-EM / SPA / Salmonella / MOTOR PROTEIN
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 4.0 Å
AuthorsYamaguchi T / Namba K / Minamino T / Kato T
Funding support Japan, 10 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP25000013MEXT Japan
Japan Society for the Promotion of Science (JSPS)JP15H01640 Japan
Japan Society for the Promotion of Science (JSPS)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)JP20H05532 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117
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 / Namba K / Minamino T / Kato T
History
DepositionOct 8, 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_61835.png

Downloads & links

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Map

FileDownload / File: emd_61835.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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00192
Minimum - Maximum-0.008653386 - 0.013387247
Average (Standard dev.)0.00005577166 (±0.0005854103)
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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Half map: #1

Fileemd_61835_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61835_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polyrod-P ring complex from Salmonella enterica subsp. enterica s...

EntireName: Polyrod-P ring complex from Salmonella enterica subsp. enterica serovar Typhimurium HK26292 mutant
Components
  • Complex: Polyrod-P ring complex from Salmonella enterica subsp. enterica serovar Typhimurium HK26292 mutant

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Supramolecule #1: Polyrod-P ring complex from Salmonella enterica subsp. enterica s...

SupramoleculeName: Polyrod-P ring complex from Salmonella enterica subsp. enterica serovar Typhimurium HK26292 mutant
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Experimental details

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Structure determination

Methodnegative staining, cryo 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-X100

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: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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
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

Particle selectionNumber selected: 386473
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 85119
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.1)

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