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- EMDB-8398: Single particle cryo-EM reconstruction of the Salmonella SPI-1 ty... -

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Basic information

Entry
Database: EMDB / ID: 8398
TitleSingle particle cryo-EM reconstruction of the Salmonella SPI-1 type III secretion injectisome basal body at 4.3 Angstrom resolutionType three secretion system
Map data24-fold averaged map of the basal body complex
SampleType III secretion injectisome basal bodyType three secretion system:
Lipoprotein PrgK / Protein PrgH
Function / homologySecretory protein YscJ/FliF / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH / Type III secretion system, PrgH/EprH-like / Secretory protein of YscJ/FliF family / Type III secretion system protein PrgH-EprH (PrgH) / Prokaryotic membrane lipoprotein lipid attachment site profile. / protein secretion / cell outer membrane / pathogenesis ...Secretory protein YscJ/FliF / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH / Type III secretion system, PrgH/EprH-like / Secretory protein of YscJ/FliF family / Type III secretion system protein PrgH-EprH (PrgH) / Prokaryotic membrane lipoprotein lipid attachment site profile. / protein secretion / cell outer membrane / pathogenesis / integral component of membrane / plasma membrane / Protein PrgH / Lipoprotein PrgK
Function and homology information
SourceSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsWorrall LJ / Hong C / Vuckovic M / Bergeron JRC / Huang RK / Yu Z / Strynadka NCJ
CitationJournal: Nature / Year: 2016
Title: Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.
Authors: L J Worrall / C Hong / M Vuckovic / W Deng / J R C Bergeron / D D Majewski / R K Huang / T Spreter / B B Finlay / Z Yu / N C J Strynadka
Validation ReportPDB-ID: 5tcp

SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2016 / Header (metadata) release: Nov 9, 2016 / Map release: Dec 21, 2016 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5tcp
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5tcp
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5tcp
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8398.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.71 Å/pix.
= 513. Å
300 pix
1.71 Å/pix.
= 513. Å
300 pix
1.71 Å/pix.
= 513. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.2226074 - 0.2467463
Average (Standard dev.)0.0002957704 (0.011063291)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.0.0.
Limit299.299.299.
Spacing300300300
CellA=B=C: 513.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z513.000513.000513.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2230.2470.000

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Supplemental data

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Sample components

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Entire Type III secretion injectisome basal body

EntireName: Type III secretion injectisome basal body / Details: PrgH130-392 mutant / Number of components: 3

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Component #1: protein, Type III secretion injectisome basal body

ProteinName: Type III secretion injectisome basal bodyType three secretion system
Details: PrgH130-392 mutant / Recombinant expression: No
MassTheoretical: 2 MDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #2: protein, Lipoprotein PrgK

ProteinName: Lipoprotein PrgK / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 26.199723 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Component #3: protein, Protein PrgH

ProteinName: Protein PrgH / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 30.360537 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 solutionSpecimen conc.: 10 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %

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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: 1.3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 64000. X (nominal), 29240. X (calibrated) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm / Energy filter: Gatan GIF / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.0 - 80.0 K)
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2515 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C24 (24 fold cyclic) / Number of projections: 67800
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Limited frequency refinement in Frealign

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Atomic model buiding

Modeling #1Refinement space: REAL
Details: Initial fitting was carried out with Chimera, followed by rebuilding and refinement in Rosetta, Phenix, and Coot.
Output model

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