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- EMDB-4733: Improved map of the FliPQR complex that forms the core of the Sal... -

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Basic information

Entry
Database: EMDB / ID: EMD-4733
TitleImproved map of the FliPQR complex that forms the core of the Salmonella type III secretion system export apparatus.Type three secretion system
Map dataType three secretion system
SampleComplex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliRType three secretion system
  • (Flagellar biosynthetic protein ...) x 3
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum assembly / protein secretion / protein targeting / integral component of membrane / plasma membrane
Type III secretion system inner membrane P protein / Flagellar transport protein FliP / Bacterial export proteins, family 3 / Bacterial export proteins, family 1 / FliP family / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Bacterial export protein family 3 / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Flagella transport protein fliP family signature 1.
Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Biological speciesSalmonella enterica (bacteria) / Salmonella enterica subsp. enterica (bacteria) / Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsJohnson S / Kuhlen L / Abrusci P / Lea SM
Citation
Journal: To Be Published
Title: The structure of an injectisome export gate demonstrates conservation of architecture in the core complexes between flagellar and virulence type III secretion systems
Authors: Johnson S / Kuhlen L / Deme J / Abrusci P / Lea SM
#1: Journal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structure of the core of the type III secretion system export apparatus.
Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / Carol V Robinson / Susan M Lea /
Abstract: Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are ...Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. Here, we present the cryoelectron microscopy structure of the Salmonella Typhimurium FliP-FliQ-FliR complex at 4.2 Å. None of the subunits adopt canonical integral membrane protein topologies, and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems, combined with cross-linking, localize the export gate as a core component of the periplasmic portion of the machinery. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream.
Validation ReportPDB-ID: 6r69

SummaryFull reportAbout validation report
DateDeposition: Mar 26, 2019 / Header (metadata) release: Dec 6, 2017 / Map release: May 29, 2019 / Update: May 29, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6r69
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4733.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 288 pix.
= 244.8 Å
0.85 Å/pix.
x 288 pix.
= 244.8 Å
0.85 Å/pix.
x 288 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.025573745 - 0.057489432
Average (Standard dev.)-0.000019648653 (±0.0024504354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z244.800244.800244.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0260.057-0.000

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Supplemental data

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Mask #1

Fileemd_4733_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Complex of the flagellar type III secretion system export apparat...

EntireName: Complex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliRType three secretion system
Number of components: 4

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Component #1: protein, Complex of the flagellar type III secretion system expor...

ProteinName: Complex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliRType three secretion system
Recombinant expression: No
MassExperimental: 195 MDa
SourceSpecies: Salmonella enterica (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: Mt56

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Component #2: protein, Flagellar biosynthetic protein FliP

ProteinName: Flagellar biosynthetic protein FliP / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 26.769021 kDa
SourceSpecies: Salmonella enterica subsp. enterica (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Flagellar biosynthetic protein FliR

ProteinName: Flagellar biosynthetic protein FliR / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.06918 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Flagellar biosynthetic protein FliQ

ProteinName: Flagellar biosynthetic protein FliQ / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 9.606758 kDa
SourceSpecies: Salmonella enterica (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 50 e/Å2 / Illumination mode: SPOT SCAN
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisition #1Number of digital images: 401
Image acquisition #2Number of digital images: 1687

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 97719 / Details: Images from K2 were also added.
3D reconstructionSoftware: RELION / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 6F2D
Output model

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