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- EMDB-10149: Structure of the RBM2 inner ring of Salmonella flagella MS-ring p... -

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Basic information

Entry
Database: EMDB / ID: EMD-10149
TitleStructure of the RBM2 inner ring of Salmonella flagella MS-ring protein FliF with 22-fold symmetry applied
Map dataPost processed map
Sample
  • Complex: Homomeric 34mer of Salmonella enterica serovar Typhimurium FliF - 22fold symmetric RBM2inner ring
    • Protein or peptide: Flagellar M-ring protein
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJohnson S / Fong YH / Deme JC / Furlong EJ / Kuhlen L / Lea SM
Funding support United Kingdom, 5 items
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, 2019-
Header (metadata) releaseMar 18, 2020-
Map releaseMar 18, 2020-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-6sd5
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_10149.png

Downloads & links

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Map

FileDownload / File: emd_10149.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost processed map
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.042903952 - 0.07938133
Average (Standard dev.)5.3808024e-05 (±0.0013941323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 355.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z355.104355.104355.104
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0430.0790.000

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Supplemental data

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Mask #1

Fileemd_10149_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refinement map

Fileemd_10149_additional.map
AnnotationRefinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_10149_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_10149_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homomeric 34mer of Salmonella enterica serovar Typhimurium FliF -...

EntireName: Homomeric 34mer of Salmonella enterica serovar Typhimurium FliF - 22fold symmetric RBM2inner ring
Components
  • Complex: Homomeric 34mer of Salmonella enterica serovar Typhimurium FliF - 22fold symmetric RBM2inner ring
    • Protein or peptide: Flagellar M-ring protein

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Supramolecule #1: Homomeric 34mer of Salmonella enterica serovar Typhimurium FliF -...

SupramoleculeName: Homomeric 34mer of Salmonella enterica serovar Typhimurium FliF - 22fold symmetric RBM2inner ring
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 2.08 MDa

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Macromolecule #1: Flagellar M-ring protein

MacromoleculeName: Flagellar M-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 61.295645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE ...String:
MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE QKSPSASVTV TLEPGRALDE GQISAVVHLV SSAVAGLPPG NVTLVDQSGH LLTQSNTSGR DLNDAQLKFA ND VESRIQR RIEAILSPIV GNGNVHAQVT AQLDFANKEQ TEEHYSPNGD ASKATLRSRQ LNISEQVGAG YPGGVPGALS NQP APPNEA PIATPPTNQQ NAQNTPQTST STNSNSAGPR STQRNETSNY EVDRTIRHTK MNVGDIERLS VAVVVNYKTL ADGK PLPLT ADQMKQIEDL TREAMGFSDK RGDTLNVVNS PFSAVDNTGG ELPFWQQQSF IDQLLAAGRW LLVLVVAWIL WRKAV RPQL TRRVEEAKAA QEQAQVRQET EEAVEVRLSK DEQLQQRRAN QRLGAEVMSQ RIREMSDNDP RVVALVIRQW MSNDHE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

10147

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C22 (22 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 87107
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6scn


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6sd5:
Structure of the RBM2 inner ring of Salmonella flagella MS-ring protein FliF with 22-fold symmetry applied

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