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- EMDB-10561: Structure of the RBM3/collar region of the Salmonella flagella MS... -

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Basic information

Entry
Database: EMDB / ID: EMD-10561
TitleStructure of the RBM3/collar region of the Salmonella flagella MS-ring protein FliF with 35-fold symmetry applied
Map dataPost process map
Sample
  • Complex: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF
    • Protein or peptide: Flagellar MS-ring FliF
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsJohnson S / Fong YH / Deme JC / Furlong EJ / Kuhlen L / Lea SM
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Wellcome Trust100298 United Kingdom
Wellcome Trust201536 United Kingdom
Wellcome Trust209194 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/M011984/1 United Kingdom
Wellcome Trust1009136 United Kingdom
Wolfson FoundationWL160052 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
DepositionDec 19, 2019-
Header (metadata) releaseMar 18, 2020-
Map releaseMar 18, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10561.png

Downloads & links

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Map

FileDownload / File: emd_10561.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost process map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 432 pix.
= 355.104 Å		0.82 Å/pix.
x 432 pix.
= 355.104 Å		0.82 Å/pix.
x 432 pix.
= 355.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.023238972 - 0.031563114
Average (Standard dev.)0.0001327079 (±0.001161312)
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
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0230.0320.000

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Supplemental data

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Mask #1

Fileemd_10561_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Refinement map

Fileemd_10561_additional.map
AnnotationRefinement map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Refinement map

Fileemd_10561_additional_1.map
AnnotationRefinement map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_10561_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_10561_half_map_2.map
AnnotationHalf map 2
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AxesZYX

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Sample components

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Entire : Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF

EntireName: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF
Components
  • Complex: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF
    • Protein or peptide: Flagellar MS-ring FliF

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Supramolecule #1: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF

SupramoleculeName: Homomeric 35mer of Salmonella enterica serovar Typhimurium FliF
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21
Molecular weightTheoretical: 2.14 MDa

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Macromolecule #1: Flagellar MS-ring FliF

MacromoleculeName: Flagellar MS-ring FliF / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQ LTQMNIPYRF ANGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE K FGISQFSE QVNYQRALEG ELARTIETLG PVKSARVHLA MPKPSLFVRE ...String:
MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQ LTQMNIPYRF ANGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE K FGISQFSE QVNYQRALEG ELARTIETLG PVKSARVHLA MPKPSLFVRE QKSPSASVTV TL EPGRALD EGQISAVVHL VSSAVAGLPP GNVTLVDQSG HLLTQSNTSG RDLNDAQLKF AND VESRIQ RRIEAILSPI VGNGNVHAQV TAQLDFANKE QTEEHYSPNG DASKATLRSR QLNI SEQVG AGYPGGVPGA LSNQPAPPNE APIATPPTNQ QNAQNTPQTS TSTNSNSAGP RSTQR NETS NYEVDRTIRH TKMNVGDIER LSVAVVVNYK TLADGKPLPL TADQMKQIED LTREAM GFS DKRGDTLNVV NSPFSAVDNT GGELPFWQQQ SFIDQLLAAG RWLLVLVVAW ILWRKAV RP QLTRRVEEAK AAQEQAQVRQ ETEEAVEVRL SKDEQLQQRR ANQRLGAEVM SQRIREMS D NDPRVVALVI RQWMSNDHE

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

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Image processing

Final reconstructionApplied symmetry - Point group: C35 (35 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 42165
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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