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- PDB-8upl: Cryo-EM structure of a Clockwise locked form of the Salmonella en... -

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Basic information

Entry
Database: PDB / ID: 8upl
TitleCryo-EM structure of a Clockwise locked form of the Salmonella enterica Typhimurium flagellar C-ring, with C34 symmetry applied
Components
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliGFlagellar motor switch protein
  • Flagellar motor switch protein FliMFlagellar motor switch protein
  • Flagellar motor switch protein FliNFlagellar motor switch protein
KeywordsMOTOR PROTEIN / Flagella / Salmonella / C-ring / motor
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 FliG / Flagellar motor switch protein FliM / 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 ...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 FliG / Flagellar motor switch protein FliM / 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 / Flagellar motor switch protein FliM / FliG middle domain / FliG N-terminal domain / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / 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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsJohnson, S. / Deme, J.C. / Lea, S.M.
Funding support United States, United Kingdom, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Wellcome Trust201536 United Kingdom
Wellcome Trust219477 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: Nat Microbiol / Year: 2024
Title: Structural basis of directional switching by the bacterial flagellum.
Authors: Steven Johnson / Justin C Deme / Emily J Furlong / Joseph J E Caesar / Fabienne F V Chevance / Kelly T Hughes / Susan M Lea /
Abstract: The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar ...The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotAB stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.
History
DepositionOct 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Flagellar M-ring protein
B1: Flagellar motor switch protein FliG
C1: Flagellar motor switch protein FliM
D1: Flagellar motor switch protein FliN
E1: Flagellar motor switch protein FliN
F1: Flagellar motor switch protein FliN
A2: Flagellar M-ring protein
B2: Flagellar motor switch protein FliG
C2: Flagellar motor switch protein FliM
D2: Flagellar motor switch protein FliN
E2: Flagellar motor switch protein FliN
F2: Flagellar motor switch protein FliN
A3: Flagellar M-ring protein
B3: Flagellar motor switch protein FliG
C3: Flagellar motor switch protein FliM
D3: Flagellar motor switch protein FliN
E3: Flagellar motor switch protein FliN
F3: Flagellar motor switch protein FliN
A4: Flagellar M-ring protein
B4: Flagellar motor switch protein FliG
C4: Flagellar motor switch protein FliM
D4: Flagellar motor switch protein FliN
E4: Flagellar motor switch protein FliN
F4: Flagellar motor switch protein FliN
A5: Flagellar M-ring protein
B5: Flagellar motor switch protein FliG
C5: Flagellar motor switch protein FliM
D5: Flagellar motor switch protein FliN
E5: Flagellar motor switch protein FliN
F5: Flagellar motor switch protein FliN
A6: Flagellar M-ring protein
B6: Flagellar motor switch protein FliG
C6: Flagellar motor switch protein FliM
D6: Flagellar motor switch protein FliN
E6: Flagellar motor switch protein FliN
F6: Flagellar motor switch protein FliN
A7: Flagellar M-ring protein
B7: Flagellar motor switch protein FliG
C7: Flagellar motor switch protein FliM
D7: Flagellar motor switch protein FliN
E7: Flagellar motor switch protein FliN
F7: Flagellar motor switch protein FliN
A8: Flagellar M-ring protein
B8: Flagellar motor switch protein FliG
C8: Flagellar motor switch protein FliM
D8: Flagellar motor switch protein FliN
E8: Flagellar motor switch protein FliN
F8: Flagellar motor switch protein FliN
A9: Flagellar M-ring protein
B9: Flagellar motor switch protein FliG
C9: Flagellar motor switch protein FliM
D9: Flagellar motor switch protein FliN
E9: Flagellar motor switch protein FliN
F9: Flagellar motor switch protein FliN
AA: Flagellar M-ring protein
BA: Flagellar motor switch protein FliG
CA: Flagellar motor switch protein FliM
DA: Flagellar motor switch protein FliN
EA: Flagellar motor switch protein FliN
FA: Flagellar motor switch protein FliN
AB: Flagellar M-ring protein
BB: Flagellar motor switch protein FliG
CB: Flagellar motor switch protein FliM
DB: Flagellar motor switch protein FliN
EB: Flagellar motor switch protein FliN
FB: Flagellar motor switch protein FliN
AC: Flagellar M-ring protein
BC: Flagellar motor switch protein FliG
CC: Flagellar motor switch protein FliM
DC: Flagellar motor switch protein FliN
EC: Flagellar motor switch protein FliN
FC: Flagellar motor switch protein FliN
AD: Flagellar M-ring protein
BD: Flagellar motor switch protein FliG
CD: Flagellar motor switch protein FliM
DD: Flagellar motor switch protein FliN
ED: Flagellar motor switch protein FliN
FD: Flagellar motor switch protein FliN
AE: Flagellar M-ring protein
BE: Flagellar motor switch protein FliG
CE: Flagellar motor switch protein FliM
DE: Flagellar motor switch protein FliN
EE: Flagellar motor switch protein FliN
FE: Flagellar motor switch protein FliN
AF: Flagellar M-ring protein
BF: Flagellar motor switch protein FliG
CF: Flagellar motor switch protein FliM
DF: Flagellar motor switch protein FliN
EF: Flagellar motor switch protein FliN
FF: Flagellar motor switch protein FliN
AG: Flagellar M-ring protein
BG: Flagellar motor switch protein FliG
CG: Flagellar motor switch protein FliM
DG: Flagellar motor switch protein FliN
EG: Flagellar motor switch protein FliN
FG: Flagellar motor switch protein FliN
AH: Flagellar M-ring protein
BH: Flagellar motor switch protein FliG
CH: Flagellar motor switch protein FliM
DH: Flagellar motor switch protein FliN
EH: Flagellar motor switch protein FliN
FH: Flagellar motor switch protein FliN
AI: Flagellar M-ring protein
BI: Flagellar motor switch protein FliG
CI: Flagellar motor switch protein FliM
DI: Flagellar motor switch protein FliN
EI: Flagellar motor switch protein FliN
FI: Flagellar motor switch protein FliN
AJ: Flagellar M-ring protein
BJ: Flagellar motor switch protein FliG
CJ: Flagellar motor switch protein FliM
DJ: Flagellar motor switch protein FliN
EJ: Flagellar motor switch protein FliN
FJ: Flagellar motor switch protein FliN
AK: Flagellar M-ring protein
BK: Flagellar motor switch protein FliG
CK: Flagellar motor switch protein FliM
DK: Flagellar motor switch protein FliN
EK: Flagellar motor switch protein FliN
FK: Flagellar motor switch protein FliN
AL: Flagellar M-ring protein
BL: Flagellar motor switch protein FliG
CL: Flagellar motor switch protein FliM
DL: Flagellar motor switch protein FliN
EL: Flagellar motor switch protein FliN
FL: Flagellar motor switch protein FliN
AM: Flagellar M-ring protein
BM: Flagellar motor switch protein FliG
CM: Flagellar motor switch protein FliM
DM: Flagellar motor switch protein FliN
EM: Flagellar motor switch protein FliN
FM: Flagellar motor switch protein FliN
AN: Flagellar M-ring protein
BN: Flagellar motor switch protein FliG
CN: Flagellar motor switch protein FliM
DN: Flagellar motor switch protein FliN
EN: Flagellar motor switch protein FliN
FN: Flagellar motor switch protein FliN
AO: Flagellar M-ring protein
BO: Flagellar motor switch protein FliG
CO: Flagellar motor switch protein FliM
DO: Flagellar motor switch protein FliN
EO: Flagellar motor switch protein FliN
FO: Flagellar motor switch protein FliN
AP: Flagellar M-ring protein
BP: Flagellar motor switch protein FliG
CP: Flagellar motor switch protein FliM
DP: Flagellar motor switch protein FliN
EP: Flagellar motor switch protein FliN
FP: Flagellar motor switch protein FliN
AQ: Flagellar M-ring protein
BQ: Flagellar motor switch protein FliG
CQ: Flagellar motor switch protein FliM
DQ: Flagellar motor switch protein FliN
EQ: Flagellar motor switch protein FliN
FQ: Flagellar motor switch protein FliN
AR: Flagellar M-ring protein
BR: Flagellar motor switch protein FliG
CR: Flagellar motor switch protein FliM
DR: Flagellar motor switch protein FliN
ER: Flagellar motor switch protein FliN
FR: Flagellar motor switch protein FliN
AS: Flagellar M-ring protein
BS: Flagellar motor switch protein FliG
CS: Flagellar motor switch protein FliM
DS: Flagellar motor switch protein FliN
ES: Flagellar motor switch protein FliN
FS: Flagellar motor switch protein FliN
AT: Flagellar M-ring protein
BT: Flagellar motor switch protein FliG
CT: Flagellar motor switch protein FliM
DT: Flagellar motor switch protein FliN
ET: Flagellar motor switch protein FliN
FT: Flagellar motor switch protein FliN
AU: Flagellar M-ring protein
BU: Flagellar motor switch protein FliG
CU: Flagellar motor switch protein FliM
DU: Flagellar motor switch protein FliN
EU: Flagellar motor switch protein FliN
FU: Flagellar motor switch protein FliN
AV: Flagellar M-ring protein
BV: Flagellar motor switch protein FliG
CV: Flagellar motor switch protein FliM
DV: Flagellar motor switch protein FliN
EV: Flagellar motor switch protein FliN
FV: Flagellar motor switch protein FliN
AW: Flagellar M-ring protein
BW: Flagellar motor switch protein FliG
CW: Flagellar motor switch protein FliM
DW: Flagellar motor switch protein FliN
EW: Flagellar motor switch protein FliN
FW: Flagellar motor switch protein FliN
AX: Flagellar M-ring protein
BX: Flagellar motor switch protein FliG
CX: Flagellar motor switch protein FliM
DX: Flagellar motor switch protein FliN
EX: Flagellar motor switch protein FliN
FX: Flagellar motor switch protein FliN
AY: Flagellar M-ring protein
BY: Flagellar motor switch protein FliG
CY: Flagellar motor switch protein FliM
DY: Flagellar motor switch protein FliN
EY: Flagellar motor switch protein FliN
FY: Flagellar motor switch protein FliN


Theoretical massNumber of molelcules
Total (without water)6,128,632204
Polymers6,128,632204
Non-polymers00
Water0
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 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 (bacteria)
References: UniProt: P15928
#2: Protein ...
Flagellar motor switch protein FliG / Flagellar motor switch protein


Mass: 36651.688 Da / Num. of mol.: 34 / Mutation: delta169-171 (PAA) / Source method: isolated from a natural source
Details: Residues 169-171 (PAA) were deleted on the chromosome.
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P0A1J9
#3: Protein ...
Flagellar motor switch protein FliM / Flagellar motor switch protein


Mass: 37901.066 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P26418
#4: Protein ...
Flagellar motor switch protein FliN / Flagellar motor switch protein


Mass: 14801.823 Da / Num. of mol.: 102 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (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: Intact C34 flagellar C-ring from purified basal bodies, clockwise locked.
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 58.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5084 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19363 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 404.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029246602
ELECTRON MICROSCOPYf_angle_d0.6706333642
ELECTRON MICROSCOPYf_chiral_restr0.044639814
ELECTRON MICROSCOPYf_plane_restr0.004343588
ELECTRON MICROSCOPYf_dihedral_angle_d4.557533830

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