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- PDB-6sd4: Structure of the RBM3/collar region of the Salmonella flagella MS... -

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Basic information

Entry
Database: PDB / ID: 6sd4
TitleStructure of the RBM3/collar region of the Salmonella flagella MS-ring protein FliF with 34-fold symmetry applied
ComponentsFlagellar M-ring protein
KeywordsMOTOR PROTEIN / Flagella / Secretion / Rotor / MS-ring / C-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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsJohnson, S. / Fong, Y.H. / Deme, J.C. / Furlong, E.J. / Kuhlen, L. / Lea, S.M.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M011984 United Kingdom
Wellcome Trust209194 United Kingdom
Wellcome Trust201536 United Kingdom
Wolfson FoundationWL160052 United Kingdom
Wellcome Trust109136 United Kingdom
CitationJournal: Nat Microbiol / Year: 2020
Title: Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation.
Authors: Steven Johnson / Yu Hang Fong / Justin C Deme / Emily J Furlong / Lucas Kuhlen / Susan M Lea /
Abstract: The bacterial flagellum is a complex self-assembling nanomachine that confers motility to the cell. Despite great variation across species, all flagella are ultimately constructed from a helical ...The bacterial flagellum is a complex self-assembling nanomachine that confers motility to the cell. Despite great variation across species, all flagella are ultimately constructed from a helical propeller that is attached to a motor embedded in the inner membrane. The motor consists of a series of stator units surrounding a central rotor made up of two ring complexes, the MS-ring and the C-ring. Despite many studies, high-resolution structural information is still lacking for the MS-ring of the rotor, and proposed mismatches in stoichiometry between the two rings have long provided a source of confusion for the field. Here, we present structures of the Salmonella MS-ring, revealing a high level of variation in inter- and intrachain symmetry that provides a structural explanation for the ability of the MS-ring to function as a complex and elegant interface between the two main functions of the flagellum-protein secretion and rotation.
History
DepositionJul 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
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)2,084,05234
Polymers2,084,05234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area144380 Å2
ΔGint-300 kcal/mol
Surface area232120 Å2
MethodPISA

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Components

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


Mass: 61295.645 Da / Num. of mol.: 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliF, fla AII.1, fla BI, STM1969 / Production host: Escherichia coli BL21(DE3) (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: Homomeric 34mer of Salmonella enterica serovar Typhimurium FliF - 34fold symmetric RBM3/collar region
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.08 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
EM software
IDNameVersionCategory
12RELION33D reconstruction
13PHENIX1.15.2-3472model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C34 (34 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140606 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6SCN

6scn


Pdb chain-ID: A / Accession code: 6SCN / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009540970
ELECTRON MICROSCOPYf_angle_d0.657355216
ELECTRON MICROSCOPYf_chiral_restr0.04136324
ELECTRON MICROSCOPYf_plane_restr0.00387412
ELECTRON MICROSCOPYf_dihedral_angle_d15.229425602

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