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- EMDB-4173: A FliPQR complex forms the core of the Salmonella type III secret... -

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Basic information

Entry
Database: EMDB / ID: 4173
TitleA FliPQR complex forms the core of the Salmonella type III secretion system export apparatus.Type three secretion system
Map dataPost-processed (B-factor sharpened and masked) map
SampleComplex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliRType three secretion system
  • (Flagellar biosynthetic protein ...) x 3
Function / homologyFlagellar biosynthesis protein FliR / Flagellar transport protein FliP / Bacterial export proteins, family 3 / Bacterial export proteins, family 1 / FliP family / Flagellar biosynthesis protein FliQ / Type III secretion system inner membrane P protein / Bacterial export protein family 3 / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein ...Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Bacterial export proteins, family 3 / Bacterial export proteins, family 1 / FliP family / Flagellar biosynthesis protein FliQ / Type III secretion system inner membrane P protein / 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. / bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum assembly / protein secretion / protein targeting / integral component of membrane / plasma membrane / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Function and homology information
SourceSalmonella enterica (bacteria) / Salmonella enterica subsp. enterica (bacteria) / Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsJohnson S / Kuhlen L / Abrusci P / Lea SM
CitationJournal: 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
Validation ReportPDB-ID: 6f2d

SummaryFull reportAbout validation report
DateDeposition: Nov 24, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Jul 4, 2018 / Last update: Jul 25, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6f2d
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4173.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
0.86 Å/pix.
= 220.16 Å
256 pix
0.86 Å/pix.
= 220.16 Å
256 pix
0.86 Å/pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.1337746 - 0.2577469
Average (Standard dev.)0.002151701 (0.012342309)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z220.160220.160220.160
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1340.2580.002

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Supplemental data

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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 FliR
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
Details: Residues 265 onwards constitute the Twin-Strep tag used for purification
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 subsp. enterica serovar Typhimurium (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: 5 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: 97718 / Details: Images from K2 were also added.
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

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