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- EMDB-12190: In situ assembled Salmonella FlgD hook cap complex -

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Basic information

Entry
Database: EMDB / ID: EMD-12190
TitleIn situ assembled Salmonella FlgD hook cap complex
Map datarefinement volume
Sample
  • Complex: Flagellar FlgD hook cap complex
    • Protein or peptide: Basal-body rod modification protein FlgD
Keywordsbacterial flagellum hook cap salmonella flagellar assembly / MEMBRANE PROTEIN
Function / homologyFlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / bacterial-type flagellum organization / bacterial-type flagellum-dependent swarming motility / Basal-body rod modification protein FlgD
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJohnson S / Furlong E
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 11, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing 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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  • Surface view with fitted model
  • Atomic models: PDB-7bhq
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bhq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12190.png

Downloads & links

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Map

FileDownload / File: emd_12190.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefinement volume
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.02024237 - 0.041165408
Average (Standard dev.)-0.00017404836 (±0.0016742742)
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-0.0200.041-0.000

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Supplemental data

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Mask #1

Fileemd_12190_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: post processed volume

Fileemd_12190_additional_1.map
Annotationpost processed volume
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_12190_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_12190_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Flagellar FlgD hook cap complex

EntireName: Flagellar FlgD hook cap complex
Components
  • Complex: Flagellar FlgD hook cap complex
    • Protein or peptide: Basal-body rod modification protein FlgD

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Supramolecule #1: Flagellar FlgD hook cap complex

SupramoleculeName: Flagellar FlgD hook cap complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)

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Macromolecule #1: Basal-body rod modification protein FlgD

MacromoleculeName: Basal-body rod modification protein FlgD / type: protein_or_peptide / ID: 1 / Details: FlgD / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Molecular weightTheoretical: 24.001637 KDa
SequenceString: MSIAVNMNDP TNTGVKTTTG SGSMTGSNAA DLQSSFLTLL VAQLKNQDPT NPLQNNELTT QLAQISTVSG IEKLNTTLGA ISGQIDNSQ SLQATTLIGH GVMVPGTTIL AGKGAEEGAV TSTTPFGVEL QQPADKVTAT ITDKDGRVVR TLEIGELRAG V HTFTWDGK ...String:
MSIAVNMNDP TNTGVKTTTG SGSMTGSNAA DLQSSFLTLL VAQLKNQDPT NPLQNNELTT QLAQISTVSG IEKLNTTLGA ISGQIDNSQ SLQATTLIGH GVMVPGTTIL AGKGAEEGAV TSTTPFGVEL QQPADKVTAT ITDKDGRVVR TLEIGELRAG V HTFTWDGK QTDGTTVPNG SYNIAITASN GGTQLVAQPL QFALVQGVTK GSNGNLLDLG TYGTTTLDEV RQII

UniProtKB: Basal-body rod modification protein FlgD

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 29748
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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