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- PDB-8wk4: Cryo-EM structure of the MS ring with FlgB and FliE within the fl... -

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Basic information

Entry
Database: PDB / ID: 8wk4
TitleCryo-EM structure of the MS ring with FlgB and FliE within the flagellar motor-hook complex in the CW state.
Components
  • Flagellar M-ring protein
  • Flagellar basal body rod protein FlgB
  • Flagellar hook-basal body complex protein FliE
KeywordsMOTOR PROTEIN / Flagellum / Flagellar motor / MS ring
Function / homology
Function and homology information


bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal ...Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar M-ring protein / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)U23A20163 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the MS ring with FlgB and FliE within the flagellar motor-hook complex in the CW state.
Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
History
DepositionSep 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,226,30345
Polymers2,226,30345
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Flagellar hook-basal body complex protein FliE


Mass: 11087.662 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P26462
#2: Protein
Flagellar basal body rod protein FlgB / Putative proximal rod protein


Mass: 15145.061 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16437
#3: Protein ...
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P15928

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C ring-containing flagellar motor-hook complex in the CW state
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
111.7 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
24.17 mMethylenediaminetetraacetic acidEDTA1
30.083 % v/voctylphenol ethoxylateTX-1001
425 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample was prepared by incubating the C ring-containing flagellar motor-hook complex with the constitutively active mutant of CheY (CheY**)
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Blot time: 4 Blot force: 10 Wait time: 30 Blot total: 1 Drain time: 2

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
2EPUimage acquisition
4cryoSPARC4.1.1CTF correction
7UCSF Chimera1.17model fitting
8UCSF ChimeraX1.5model fitting
9Coot0.9.8.7model fitting
11cryoSPARC4.1.1initial Euler assignment
12cryoSPARC4.1.1final Euler assignment
14cryoSPARC4.1.13D reconstruction
15PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 46058 / Details: Particles were manually picked using cryoSPARC
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24190 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingDetails: Model-Angelo / Source name: Other / Type: in silico model

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