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

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Basic information

Entry
Database: PDB / ID: 9jqo
TitlePolyrod formed by FlgG (G65V) from the Salmonella TH26292 strain
ComponentsFlagellar basal-body rod protein FlgG
KeywordsMOTOR PROTEIN / flagella motor. polyrod / P ring on polyrod complex / Cryo-EM / SPA / Salmonella
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)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / cryo EM / Resolution: 3.37 Å
AuthorsYamaguchi, T. / Kato, T. / Minamino, T. / Namba, K.
Funding support Japan, 9items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar basal-body rod protein FlgG
B: Flagellar basal-body rod protein FlgG
C: Flagellar basal-body rod protein FlgG
D: Flagellar basal-body rod protein FlgG
E: Flagellar basal-body rod protein FlgG
F: Flagellar basal-body rod protein FlgG
G: Flagellar basal-body rod protein FlgG
H: Flagellar basal-body rod protein FlgG
I: Flagellar basal-body rod protein FlgG
J: Flagellar basal-body rod protein FlgG
K: Flagellar basal-body rod protein FlgG
L: Flagellar basal-body rod protein FlgG
M: Flagellar basal-body rod protein FlgG
N: Flagellar basal-body rod protein FlgG
O: Flagellar basal-body rod protein FlgG
P: Flagellar basal-body rod protein FlgG
Q: Flagellar basal-body rod protein FlgG
R: Flagellar basal-body rod protein FlgG
S: Flagellar basal-body rod protein FlgG
T: Flagellar basal-body rod protein FlgG
U: Flagellar basal-body rod protein FlgG
V: Flagellar basal-body rod protein FlgG
W: Flagellar basal-body rod protein FlgG
X: Flagellar basal-body rod protein FlgG
Y: Flagellar basal-body rod protein FlgG
Z: Flagellar basal-body rod protein FlgG
a: Flagellar basal-body rod protein FlgG
b: Flagellar basal-body rod protein FlgG
c: Flagellar basal-body rod protein FlgG
d: Flagellar basal-body rod protein FlgG
e: Flagellar basal-body rod protein FlgG
f: Flagellar basal-body rod protein FlgG
g: Flagellar basal-body rod protein FlgG
h: Flagellar basal-body rod protein FlgG
i: Flagellar basal-body rod protein FlgG
j: Flagellar basal-body rod protein FlgG
k: Flagellar basal-body rod protein FlgG
l: Flagellar basal-body rod protein FlgG
m: Flagellar basal-body rod protein FlgG
n: Flagellar basal-body rod protein FlgG
o: Flagellar basal-body rod protein FlgG
p: Flagellar basal-body rod protein FlgG
q: Flagellar basal-body rod protein FlgG
r: Flagellar basal-body rod protein FlgG
s: Flagellar basal-body rod protein FlgG
t: Flagellar basal-body rod protein FlgG
u: Flagellar basal-body rod protein FlgG
v: Flagellar basal-body rod protein FlgG


Theoretical massNumber of molelcules
Total (without water)1,335,69148
Polymers1,335,69148
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 27826.887 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Details: G65V is a natural mutation isolated from the engineered strain TH26292.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: TH26292 / Gene: flgG, fla FVII, flaL, STY1218, t1741
Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain (production host): TH26292 / References: UniProt: P0A1J4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Polyrod composed of FlgG(G65V) / Type: ORGANELLE OR CELLULAR COMPONENT
Details: Polyrod from the complex of P ring attached to polyrod. The FlgG(G65V) mutant of flagellar motor from Salmonella enterica serva typhimurium
Entity ID: all / Source: NATURAL
Molecular weightValue: 0.38 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8
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
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethaneTris-HCl1
250 mMsodium ChlorideNaCl1
325 mMImidazoleImidazole1
40.002 %Lauryl Maltose Neopentyl GlycolLMNG1
50.05 %Triton X-100Triton1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE
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.
Material: Uranyl acetate
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 277 K
Details: blotting time of 4 seconds, 1 seconds drain time, force 0

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2000 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6 sec. / Electron dose: 75 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 28712
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.

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2.0particle selection
2PHENIX1.21rc1_5127model refinement
5cryoSPARC3.2.0CTF correction
12cryoSPARC3.2.0classification
13cryoSPARC3.2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 64.9 ° / Axial rise/subunit: 4.31 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 386473
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88969 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL
Details: Phenix1.21-rc1 , refmac servalcat and ISOLDE was used for fitting, and Phenix was used for final fitting.
Atomic model buildingPDB-ID: 7CBM

7cbm


Pdb chain-ID: B / Accession code: 7CBM / Chain residue range: 1-260
Details: The initial model consisted of the whole sequence of wild type FlgG
Pdb chain residue range: 1-260 / Source name: PDB / Type: experimental model

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