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- EMDB-30941: Salmonella flagella MS-ring protein FliF 1-456 having C35 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-30941
TitleSalmonella flagella MS-ring protein FliF 1-456 having C35 symmetry
Map data
Sample
  • Complex: Salmonella flagella MS-ring protein FliF 1-456
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: 4.59 Å
AuthorsMakino F / Kawamoto A / Namba K
Funding support Japan, 13 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25000013 Japan
Japan Society for the Promotion of Science (JSPS)18K06155 Japan
Japan Society for the Promotion of Science (JSPS)20770083 Japan
Japan Society for the Promotion of Science (JSPS)18K14639 Japan
Japan Society for the Promotion of Science (JSPS)JP26293097
Japan Society for the Promotion of Science (JSPS)JP19H03182
Japan Society for the Promotion of Science (JSPS)JP15H05593
Japan Society for the Promotion of Science (JSPS)JP20K15749
Japan Society for the Promotion of Science (JSPS)JP15H02386
Japan Society for the Promotion of Science (JSPS)JP15H01640
Japan Society for the Promotion of Science (JSPS)JP20H05532
Japan Agency for Medical Research and Development (AMED)JP19am0101117
Japan Agency for Medical Research and Development (AMED)
CitationJournal: Nat Commun / Year: 2021
Title: Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries.
Authors: Akihiro Kawamoto / Tomoko Miyata / Fumiaki Makino / Miki Kinoshita / Tohru Minamino / Katsumi Imada / Takayuki Kato / Keiichi Namba /
Abstract: The bacterial flagellar MS ring is a transmembrane complex acting as the core of the flagellar motor and template for flagellar assembly. The C ring attached to the MS ring is involved in torque ...The bacterial flagellar MS ring is a transmembrane complex acting as the core of the flagellar motor and template for flagellar assembly. The C ring attached to the MS ring is involved in torque generation and rotation switch, and a large symmetry mismatch between these two rings has been a long puzzle, especially with respect to their role in motor function. Here, using cryoEM structural analysis of the flagellar basal body and the MS ring formed by full-length FliF from Salmonella enterica, we show that the native MS ring is formed by 34 FliF subunits with no symmetry variation. Symmetry analysis of the C ring shows a variation with a peak at 34-fold, suggesting flexibility in C ring assembly. Finally, our data also indicate that FliF subunits assume two different conformations, contributing differentially to the inner and middle parts of the M ring and thus resulting in 23- and 11-fold subsymmetries in the inner and middle M ring, respectively. The internal core of the M ring, formed by 23 subunits, forms a hole of the right size to accommodate the protein export gate.
History
DepositionFeb 1, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30941.png

Downloads & links

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Map

FileDownload / File: emd_30941.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.02389025 - 0.10617649
Average (Standard dev.)0.00026693448 (±0.005106865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions248248248
Spacing248248248
CellA=B=C: 496.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z248248248
origin x/y/z0.0000.0000.000
length x/y/z496.000496.000496.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS248248248
D min/max/mean-0.0240.1060.000

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Supplemental data

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Sample components

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Entire : Salmonella flagella MS-ring protein FliF 1-456

EntireName: Salmonella flagella MS-ring protein FliF 1-456
Components
  • Complex: Salmonella flagella MS-ring protein FliF 1-456

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Supramolecule #1: Salmonella flagella MS-ring protein FliF 1-456

SupramoleculeName: Salmonella flagella MS-ring protein FliF 1-456 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration4.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloridesodium chloride
25.0 mMC4H11NO3Tris-HClTris
1.0 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid
0.1 %C14H22O(C2H4O)10Triton-X100
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 40.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 0.4 µm / Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6200 / Average electron dose: 50.0 e/Å2

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Image processing

Particle selectionNumber selected: 262434
CTF correctionSoftware - Name: Warp (ver. 1.0.9)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.8)
Final 3D classificationNumber classes: 3 / Avg.num./class: 70000 / Software - Name: RELION (ver. 3.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.8)
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.8) / Number images used: 62306
FSC plot (resolution estimation)

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