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- PDB-8xp0: Cryo-EM structure of the protomers of the C ring in the CCW state -

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Basic information

Entry
Database: PDB / ID: 8xp0
TitleCryo-EM structure of the protomers of the C ring in the CCW state
Components
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliG
  • Flagellar motor switch protein FliM
  • Flagellar motor switch protein FliN
KeywordsMOTOR PROTEIN / C ring / flagellum / flagellar motor / motor / switch complex / rotation / FliF / FliG / FliM / FliN
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal ...Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / 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 motor switch protein FliG / Flagellar M-ring protein / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 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
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
National Natural Science Foundation of China (NSFC)U23A20163
CitationJournal: To Be Published
Title: Cryo-EM structure of the protomers of the C ring in the CCW state
Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
History
DepositionJan 2, 2024Deposition 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
M: Flagellar motor switch protein FliG
N: Flagellar M-ring protein
O: Flagellar motor switch protein FliM
P: Flagellar motor switch protein FliN
Q: Flagellar motor switch protein FliN
R: Flagellar motor switch protein FliN
S: Flagellar motor switch protein FliG
T: Flagellar M-ring protein
U: Flagellar motor switch protein FliM
V: Flagellar motor switch protein FliN
W: Flagellar motor switch protein FliN
X: Flagellar motor switch protein FliN
Y: Flagellar motor switch protein FliG
Z: Flagellar M-ring protein
a: Flagellar motor switch protein FliM
b: Flagellar motor switch protein FliN
c: Flagellar motor switch protein FliN
d: Flagellar motor switch protein FliN


Theoretical massNumber of molelcules
Total (without water)541,47918
Polymers541,47918
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 motor switch protein FliG


Mass: 36890.957 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J9
#2: Protein Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P15928
#3: Protein Flagellar motor switch protein FliM


Mass: 37901.066 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P26418
#4: Protein
Flagellar motor switch protein FliN


Mass: 14801.823 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P26419

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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 CCW state
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
25 mMethylenediaminetetraacetic acidEDTA1
30.1 %octylphenol ethoxylateTX-1001
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 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: 2 Blot force: -5 Wait time: 5 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
4cryoSPARC4.1.1CTF correction
7UCSF Chimera1.17model fitting
8UCSF ChimeraX1.5model fitting
9Coot0.9.8.7model fitting
11PHENIX1.20.1_4487:model refinement
12cryoSPARC4.1.1initial Euler assignment
13cryoSPARC4.1.1final Euler assignment
15cryoSPARC4.1.13D reconstruction
22EPUimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 19627 / Details: Particles were manually picked using cryoSPARC
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 667318 / Details: C34 symmetry-expanded particles / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDSource nameTypeAccession code
11AlphaFoldin silico model
21PDBexperimental model3HJL
31PDBexperimental model4FHR
41PDBexperimental model5TDY
51PDBexperimental model4YXB
61PDBexperimental model4YX1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221561
ELECTRON MICROSCOPYf_angle_d0.43629160
ELECTRON MICROSCOPYf_dihedral_angle_d8.1548346
ELECTRON MICROSCOPYf_chiral_restr0.0383489
ELECTRON MICROSCOPYf_plane_restr0.0033795

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