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- EMDB-12603: Salmonella flagellar basal body refined in C1 map -

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Basic information

Entry
Database: EMDB / ID: EMD-12603
TitleSalmonella flagellar basal body refined in C1 map
Map data
SampleSalmonella flagellar basal body
  • Flagellar M-ring protein
  • (Flagellar biosynthetic protein ...) x 3
  • Flagellar hook-basal body complex protein FliE
  • (Flagellar basal body ...) x 2
  • (Flagellar basal-body rod protein ...) x 2
  • Flagellar L-ring protein
  • Flagellar P-ring protein
  • Basal-body rod modification protein FlgD
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum organization / bacterial-type flagellum assembly / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility / protein targeting ...bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum organization / bacterial-type flagellum assembly / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility / protein targeting / motor activity / protein secretion / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity / integral component of membrane / plasma membrane
Similarity search - Function
FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / Flagellar hook capping protein / Flagellar L-ring protein / Flagellar L-ring protein / FlgD Ig-like domain / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB ...FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / Flagellar hook capping protein / Flagellar L-ring protein / Flagellar L-ring protein / FlgD Ig-like domain / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar hook-basal body complex protein FliE / Flagellar P-ring protein / Flagellar P-ring protein / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod FlgG / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Type III secretion system inner membrane R protein / Flagellar basal body rod protein, conserved site / Bacterial export proteins, family 3 / Bacterial export proteins, family 1 / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Bacterial export protein family 3 / Flagellar hook-basal body protein, FlgE/F/G / Flagella transport protein fliP family signature 1. / Flagellar M-ring C-terminal / FliP family / Flagellar M-ring protein C-terminal / Flagella transport protein fliP family signature 2. / Flagellar M-ring protein FliF / Flagellar basal body rod protein, N-terminal / Type III secretion system inner membrane P protein / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal
Similarity search - Domain/homology
Flagellar P-ring protein / Flagellar L-ring protein / Flagellar basal-body rod protein FlgG / Basal-body rod modification protein FlgD / Flagellar biosynthetic protein FliQ / Flagellar basal body protein / Flagellar basal-body rod protein FlgC / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliP ...Flagellar P-ring protein / Flagellar L-ring protein / Flagellar basal-body rod protein FlgG / Basal-body rod modification protein FlgD / Flagellar biosynthetic protein FliQ / Flagellar basal body protein / Flagellar basal-body rod protein FlgC / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR / Flagellar M-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsJohnson S / Furlong E / Lea SM
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust219477 United Kingdom
Wellcome Trust209194 United Kingdom
Wellcome Trust201536 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: Nat Microbiol / Year: 2021
Title: Molecular structure of the intact bacterial flagellar basal body.
Authors: Steven Johnson / Emily J Furlong / Justin C Deme / Ashley L Nord / Joseph J E Caesar / Fabienne F V Chevance / Richard M Berry / Kelly T Hughes / Susan M Lea /
Abstract: The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the ...The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids. Here, we present structures of the intact Salmonella flagellar basal body, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2-3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine.
History
DepositionMar 15, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nvg
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12603.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 768 pix.
= 638.976 Å
0.83 Å/pix.
x 768 pix.
= 638.976 Å
0.83 Å/pix.
x 768 pix.
= 638.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.0075 / Movie #1: 0.0075
Minimum - Maximum-0.009936759 - 0.023277827
Average (Standard dev.)-0.00010903703 (±0.0012119168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 638.976 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z638.976638.976638.976
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS768768768
D min/max/mean-0.0100.023-0.000

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Supplemental data

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Segmentation: #1

Fileemd_12603_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_12603_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_12603_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Salmonella flagellar basal body

EntireName: Salmonella flagellar basal body / Number of components: 13

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Component #1: protein, Salmonella flagellar basal body

ProteinName: Salmonella flagellar basal body / Recombinant expression: No
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #2: protein, Flagellar M-ring protein

ProteinName: Flagellar M-ring protein / Number of Copies: 34 / Recombinant expression: No
MassTheoretical: 61.295645 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #3: protein, Flagellar biosynthetic protein FliP

ProteinName: Flagellar biosynthetic protein FliP / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 26.801086 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #4: protein, Flagellar biosynthetic protein FliR

ProteinName: Flagellar biosynthetic protein FliR / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.938865 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #5: protein, Flagellar biosynthetic protein FliQ

ProteinName: Flagellar biosynthetic protein FliQ / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 9.606758 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #6: protein, Flagellar hook-basal body complex protein FliE

ProteinName: Flagellar hook-basal body complex protein FliE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 11.087662 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #7: protein, Flagellar basal body rod protein FlgB

ProteinName: Flagellar basal body rod protein FlgB / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 15.145061 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #8: protein, Flagellar basal-body rod protein FlgC

ProteinName: Flagellar basal-body rod protein FlgC / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 13.991889 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #9: protein, Flagellar basal body protein

ProteinName: Flagellar basal body protein / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 26.121223 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #10: protein, Flagellar basal-body rod protein FlgG

ProteinName: Flagellar basal-body rod protein FlgG / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 27.784807 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #11: protein, Flagellar L-ring protein

ProteinName: Flagellar L-ring protein / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 24.726666 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #12: protein, Flagellar P-ring protein

ProteinName: Flagellar P-ring protein / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 38.194176 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #13: protein, Basal-body rod modification protein FlgD

ProteinName: Basal-body rod modification protein FlgD / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 24.001637 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 59 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 60497
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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