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- PDB-7e81: Cryo-EM structure of the flagellar MS ring with FlgB-Dc loop and ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+81
TitleCryo-EM structure of the flagellar MS ring with FlgB-Dc loop and FliE-helix 1 from Salmonella
Components
  • Flagellar M-ring protein
  • FlgB-Dc loop
  • FliE helix 1
KeywordsMOTOR PROTEIN / Flagella / Motor-hook / MS ring
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / plasma membrane
Similarity search - Function
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
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsTan, J.X. / Chang, S.H. / Wang, X.F. / Xu, C.H. / Zhou, Y. / Zhang, X. / Zhu, Y.Q.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504803 China
Ministry of Science and Technology (MoST, China)2018YFA0507700 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81501717 China
CitationJournal: Cell / Year: 2021
Title: Structural basis of assembly and torque transmission of the bacterial flagellar motor.
Authors: Jiaxing Tan / Xing Zhang / Xiaofei Wang / Caihuang Xu / Shenghai Chang / Hangjun Wu / Ting Wang / Huihui Liang / Haichun Gao / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key ...The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key determinant of pathogenicity. The detailed structure of the flagellar motor remains unknown. Here we present an atomic-resolution cryoelectron microscopy (cryo-EM) structure of the bacterial flagellar motor complexed with the hook, consisting of 175 subunits with a molecular mass of approximately 6.3 MDa. The structure reveals that 10 peptides protruding from the MS ring with the FlgB and FliE subunits mediate torque transmission from the MS ring to the rod and overcome the symmetry mismatch between the rotational and helical structures in the motor. The LP ring contacts the distal rod and applies electrostatic forces to support its rotation and torque transmission to the hook. This work provides detailed molecular insights into the structure, assembly, and torque transmission mechanisms of the flagellar motor.
History
DepositionFeb 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 26, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
Da: Flagellar M-ring protein
Db: Flagellar M-ring protein
Dc: Flagellar M-ring protein
Dd: Flagellar M-ring protein
De: Flagellar M-ring protein
Df: Flagellar M-ring protein
Dg: Flagellar M-ring protein
Dh: Flagellar M-ring protein
Di: Flagellar M-ring protein
Dj: Flagellar M-ring protein
Dk: Flagellar M-ring protein
Dl: Flagellar M-ring protein
Dm: Flagellar M-ring protein
Dn: Flagellar M-ring protein
Do: Flagellar M-ring protein
Dp: Flagellar M-ring protein
Dq: Flagellar M-ring protein
Dr: Flagellar M-ring protein
Ds: Flagellar M-ring protein
Dt: Flagellar M-ring protein
Du: Flagellar M-ring protein
Dv: Flagellar M-ring protein
Dw: Flagellar M-ring protein
GA: FlgB-Dc loop
GF: FliE helix 1
GG: FliE helix 1
GH: FliE helix 1
GI: FliE helix 1
GJ: FliE helix 1
GK: FliE helix 1
GC: FlgB-Dc loop
GE: FlgB-Dc loop
GD: FlgB-Dc loop
GB: FlgB-Dc loop
Ca: Flagellar M-ring protein
Cb: Flagellar M-ring protein
Cc: Flagellar M-ring protein
Cd: Flagellar M-ring protein
Ce: Flagellar M-ring protein
Cf: Flagellar M-ring protein
cg: Flagellar M-ring protein
Ch: Flagellar M-ring protein
Ci: Flagellar M-ring protein
Cj: Flagellar M-ring protein
Ck: Flagellar M-ring protein
Cl: Flagellar M-ring protein
Cm: Flagellar M-ring protein
Cn: Flagellar M-ring protein
Co: Flagellar M-ring protein
Cp: Flagellar M-ring protein
Cq: Flagellar M-ring protein
Cr: Flagellar M-ring protein
Cs: Flagellar M-ring protein
Ct: Flagellar M-ring protein
Cu: Flagellar M-ring protein
Cv: Flagellar M-ring protein
Cw: Flagellar M-ring protein
Cx: Flagellar M-ring protein
Cy: Flagellar M-ring protein
Cz: Flagellar M-ring protein
Ea: Flagellar M-ring protein
Eb: Flagellar M-ring protein
Ec: Flagellar M-ring protein
Ed: Flagellar M-ring protein
Ee: Flagellar M-ring protein
Ef: Flagellar M-ring protein
Eg: Flagellar M-ring protein
Fh: Flagellar M-ring protein


Theoretical massNumber of molelcules
Total (without water)3,508,34868
Polymers3,508,34868
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 57 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P15928
#2: Protein/peptide
FlgB-Dc loop


Mass: 1039.273 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
#3: Protein/peptide
FliE helix 1


Mass: 1549.902 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Sequence details1. The full sequence of FlgB is listed below: ...1. The full sequence of FlgB is listed below: MLDRLDAALRFQQEALNLRAQRQEILAANIANADTPGYQARDIDFASELKKVMVRGREETGGVALTLTSSHHIPAQAVSSPAVDLLYRVPDQPSLDGNTVDMDRERTQFADNSLKYQMGLTVLGSQLKGMMNVLQGGN The FlgB-Dc loop is a fragment of FlgB, but the residues in chains GA/GB/GC/GD/GE could not be precisely built due to their low densities.The residues of FlgB-Dc loop are likely located between the residues of 56-81 of FlgB according to its relative position. 2. The full sequence of FliE is listed below: MAAIQGIEGVISQLQATAMAARGQDTHSQSTVSFAGQLHAALDRISDRQAAARVQAEKFTLGEPGIALNDVMADMQKASVSMQMGIQVRNKLVAAYQEVMSMQV The FliE-helix 1 is a fragment of FliE, but the residues in chains GF/GG/GH/GI/GJ/GK could not be precisely built due to their low densities. The residues are likely located between the residues of 1-22 of FliE according to its relative posion.

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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: Flagellar motor-hook complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane hydrochloride-hydrochlorideTris-HClTris1
25 mMethylene diamine tetraacetic acidEDTAEthylenediaminetetraacetic acid1
30.1 %octylphenol ethoxylateTX-1001
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: blot for 6 seconds before plunging

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52714 / Symmetry type: POINT

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