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- EMDB-8545: SpaO mutant structure of Salmonella Type III secretion injectisome -

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Basic information

Entry
Database: EMDB / ID: 8545
TitleSpaO mutant structure of Salmonella Type III secretion injectisomeType three secretion system
Map dataSpaO mutant structure of Salmonella Type III secretion injectisomeType three secretion system
SampleSpaO mutant of Salmonella injectisome:
SourceSalmonella (bacteria)
Methodsubtomogram averaging / cryo EM / 30 Å resolution
AuthorsHu B / Liu J
CitationJournal: Cell / Year: 2017
Title: In Situ Molecular Architecture of the Salmonella Type III Secretion Machine.
Authors: Bo Hu / Maria Lara-Tejero / Qingke Kong / Jorge E Galán / Jun Liu
Abstract: Type III protein secretion systems have specifically evolved to deliver bacterially encoded proteins into target eukaryotic cells. The core elements of this multi-protein machine are the ...Type III protein secretion systems have specifically evolved to deliver bacterially encoded proteins into target eukaryotic cells. The core elements of this multi-protein machine are the envelope-associated needle complex, the inner membrane export apparatus, and a large cytoplasmic sorting platform. Here, we report a high-resolution in situ structure of the Salmonella Typhimurium type III secretion machine obtained by high-throughput cryo-electron tomography and sub-tomogram averaging. Through molecular modeling and comparative analysis of machines assembled with protein-tagged components or from different deletion mutants, we determined the molecular architecture of the secretion machine in situ and localized its structural components. We also show that docking of the sorting platform results in significant conformational changes in the needle complex to provide the symmetry adaptation required for the assembly of the entire secretion machine. These studies provide major insight into the structure and assembly of a broadly distributed protein secretion machine.
DateDeposition: Jan 4, 2017 / Header (metadata) release: Feb 8, 2017 / Map release: Mar 29, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.98
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.98
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_8545.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
5.2 Å/pix.
= 1040. Å
200 pix
5.2 Å/pix.
= 1040. Å
200 pix
5.2 Å/pix.
= 1040. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density
Contour Level:1.98 (by author), 1.98 (movie #1):
Minimum - Maximum-12.461525 - 13.407977000000001
Average (Standard dev.)-0.000000000129946 (1.0)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100.0-100.0-100.0
Limit99.099.099.0
Spacing200200200
CellA=B=C: 1040.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1040.0001040.0001040.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-12.46213.408-0.000

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Supplemental data

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Sample components

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Entire SpaO mutant of Salmonella injectisome

EntireName: SpaO mutant of Salmonella injectisome / Number of components: 1

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Component #1: protein, SpaO mutant of Salmonella injectisome

ProteinName: SpaO mutant of Salmonella injectisome / Recombinant expression: No
SourceSpecies: Salmonella (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: OTHER
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 766
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.5 CUT-OFF

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