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- EMDB-60995: P ring on polyrod-P ring complex from Salmonella TH26292 strain -

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Basic information

Entry
Database: EMDB / ID: EMD-60995
TitleP ring on polyrod-P ring complex from Salmonella TH26292 strain
Map data
Sample
  • Complex: P ring on polyrod-P ring complex from Salmonella typhimurium HK26292 mutant
    • Protein or peptide: Flagellar P-ring protein
Keywordsflagella motor. P ring on polyrod(PaPR) complex / Cryo-EM / SPA / Salmonella / MOTOR PROTEIN
Function / homologybacterial-type flagellum basal body, distal rod, P ring / Flagellar P-ring protein / Flagellar P-ring protein / bacterial-type flagellum-dependent cell motility / outer membrane-bounded periplasmic space / structural molecule activity / Flagellar P-ring protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.33 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 in the bacterial flagellar motor
Authors: Yamaguchi T / Kato T / Minamino T / Namba K
History
DepositionJul 30, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60995.png

Downloads & links

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Map

FileDownload / File: emd_60995.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00527
Minimum - Maximum-0.027463388 - 0.05252699
Average (Standard dev.)0.000008699599 (±0.0016999108)
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_60995_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60995_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60995_half_map_2.map
Projections & Slices
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Sample components

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Entire : P ring on polyrod-P ring complex from Salmonella typhimurium HK26...

EntireName: P ring on polyrod-P ring complex from Salmonella typhimurium HK26292 mutant
Components
  • Complex: P ring on polyrod-P ring complex from Salmonella typhimurium HK26292 mutant
    • Protein or peptide: Flagellar P-ring protein

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Supramolecule #1: P ring on polyrod-P ring complex from Salmonella typhimurium HK26...

SupramoleculeName: P ring on polyrod-P ring complex from Salmonella typhimurium HK26292 mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 0.38 kDa/nm

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Macromolecule #1: Flagellar P-ring protein

MacromoleculeName: Flagellar P-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: HK26292
Molecular weightTheoretical: 36.29982 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
SequenceString: ERIRDLTSVQ GVRENSLIGY GLVVGLDGTG DQTTQTPFTT QTLNNMLSQL GITVPTGTNM QLKNVAAVMV TASYPPFARQ GQTIDVVVS SMGNAKSLRG GTLLMTPLKG VDSQVYALAQ GNILVGGAGA SAGGSSVQVN QLNGGRITNG AIIERELPTQ F GAGNTINL ...String:
ERIRDLTSVQ GVRENSLIGY GLVVGLDGTG DQTTQTPFTT QTLNNMLSQL GITVPTGTNM QLKNVAAVMV TASYPPFARQ GQTIDVVVS SMGNAKSLRG GTLLMTPLKG VDSQVYALAQ GNILVGGAGA SAGGSSVQVN QLNGGRITNG AIIERELPTQ F GAGNTINL QLNDEDFTMA QQITDAINRA RGYGSATALD ARTVQVRVPS GNSSQVRFLA DIQNMEVNVT PQDAKVVINS RT GSVVMNR EVTLDSCAVA QGNLSVTVNR QLNVNQPNTP FGGGQTVVTP QTQIDLRQSG GSLQSVRSSA NLNSVVRALN ALG ATPMDL MSILQSMQSA GCLRAKLEII

UniProtKB: Flagellar P-ring protein

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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 mMNaClSodum Chloride
25.0 mMImidazoleImidazole
0.002 %LMNGLauryl maltose neopentyl glycol
0.05 %TritonTriton X-100
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / 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 recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Average exposure time: 6.0 sec. / #0 - Average electron dose: 75.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Average exposure time: 2.5 sec. / #1 - Average electron dose: 40.0 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 #1

Image processing ID1
Image recording ID1
Particle selectionNumber selected: 386473
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7clr

Final reconstructionApplied symmetry - Point group: C26 (26 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 85463
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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Image processing #2

Image processing ID2
Image recording ID2
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7clr

Final 3D classificationNumber classes: 1

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Atomic model buiding 1

Initial modelPDB ID:

7clr


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: PHENIX (ver. 1.21-rc)
DetailsPhenix1.21-rc1 , refmac servalcat, coot and ISOLDE was used for fitting, and Phenix was used for final fitting.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9iyc:
P ring on polyrod-P ring complex from Salmonella TH26292 strain

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