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- PDB-8xp1: Cryo-EM structure of the protomers of the C ring in the CW state -

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Basic information

Entry
Database: PDB / ID: 8xp1
TitleCryo-EM structure of the protomers of the C ring in the CW state
Components
  • Chemotaxis protein CheY
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliG
  • Flagellar motor switch protein FliM
  • Flagellar motor switch protein FliN
KeywordsMOTOR PROTEIN / Flagellum / Flagellar motor / C ring / CheY
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / phosphorelay signal transduction system / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / metal ion binding ...archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / phosphorelay signal transduction system / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / metal ion binding / plasma membrane / cytoplasm
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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Chemotaxis protein CheY / 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: 4.4 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
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 protomers of the C ring in the CW 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
0: Flagellar motor switch protein FliN
C: Flagellar M-ring protein
S: Flagellar motor switch protein FliM
Z: Flagellar motor switch protein FliG
h: Chemotaxis protein CheY
o: Flagellar motor switch protein FliN
u: Flagellar motor switch protein FliN
AA: Flagellar motor switch protein FliN
D: Flagellar M-ring protein
T: Flagellar motor switch protein FliM
a: Flagellar motor switch protein FliG
i: Chemotaxis protein CheY
p: Flagellar motor switch protein FliN
v: Flagellar motor switch protein FliN
AB: Flagellar motor switch protein FliN
E: Flagellar M-ring protein
U: Flagellar motor switch protein FliM
b: Flagellar motor switch protein FliG
j: Chemotaxis protein CheY
q: Flagellar motor switch protein FliN
w: Flagellar motor switch protein FliN


Theoretical massNumber of molelcules
Total (without water)584,01221
Polymers584,01221
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 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
#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 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
#5: Protein Chemotaxis protein CheY


Mass: 14177.512 Da / Num. of mol.: 3 / Mutation: D13K, Y106W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: cheY, STM1916 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A2D5

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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

Component
IDNameTypeEntity IDParent-IDSource
1C ring-containing flagellar motor-hook complex in the CW stateCOMPLEXall0MULTIPLE SOURCES
2Constitutively active mutant of CheYCOMPLEX#51RECOMBINANT
3C ring-containing flagellar motor-hookCELL#1-#41NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)99287
32Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)99287
Source (recombinant)Organism: Escherichia coli BL21(DE3) (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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 956046 / Details: C34 symmetry-expanded particles / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
ID 3D fitting-IDSource nameTypeAccession code
11AlphaFoldin silico model
21PDBexperimental model8XP0
31PDBexperimental model2FLW

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