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- EMDB-12183: Salmonella LP ring 26 mer refined in C26 map -

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Basic information

Entry
Database: EMDB / ID: EMD-12183
TitleSalmonella LP ring 26 mer refined in C26 map
Map data
SampleFlagellar LP ring:
Flagellar L-ring protein / Flagellar P-ring protein / YecR / (ligand) x 2
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum-dependent cell motility / motor activity / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
YecR-like lipoprotein / YecR-like lipoprotein / Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Uncharacterized protein / Flagellar L-ring protein / Flagellar P-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria) / Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 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
DepositionJan 7, 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: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bgl
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bgl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12183.map.gz / Format: CCP4 / Size: 307.5 MB / 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 432 pix.
= 359.424 Å
0.83 Å/pix.
x 432 pix.
= 359.424 Å
0.83 Å/pix.
x 432 pix.
= 359.424 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: 0.011 / Movie #1: 0.011
Minimum - Maximum-0.01927556 - 0.050039597
Average (Standard dev.)0.00025506705 (±0.0030242172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 359.424 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z359.424359.424359.424
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0190.0500.000

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Supplemental data

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Additional map: post processed

Fileemd_12183_additional_1.map
Annotationpost processed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 1

Fileemd_12183_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 2

Fileemd_12183_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Flagellar LP ring

EntireName: Flagellar LP ring / Number of components: 6

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Component #1: protein, Flagellar LP ring

ProteinName: Flagellar LP ring / Recombinant expression: No
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhi (bacteria)

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Component #2: protein, Flagellar L-ring protein

ProteinName: Flagellar L-ring protein / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 24.726666 kDa
SourceSpecies: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Component #3: protein, Flagellar P-ring protein

ProteinName: Flagellar P-ring protein / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 38.194176 kDa
SourceSpecies: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Component #4: protein, YecR

ProteinName: YecR / Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 12.194968 kDa
SourceSpecies: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Component #5: ligand, (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)eth...

LigandName: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4,5-bis(oxidanyl)oxane-2-carboxylic acid
Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 0.222193 kDa

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Component #6: ligand, [(3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-[[(2~{R},3...

LigandName: [(3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-(hydroxymethyl)-5-phosphonooxy-4-[(3~{R})-3- ...Name: [(3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-(hydroxymethyl)-5-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]oxymethyl]-5-oxidanyl-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-2-phosphonooxy-oxan-3-yl]amino]-1-oxidanylidene-tetradecan-3-yl] hexadecanoate
Number of Copies: 26 / Recombinant expression: No
MassTheoretical: 2.036774 kDa

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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 / Applied symmetry: C26 (26回回転対称) / Number of projections: 31643
3D reconstructionSoftware: RELION / Resolution: 2.2 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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