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- EMDB-8544: Salmonella Type III secretion injectisome -

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Basic information

Entry
Database: EMDB / ID: EMD-8544
TitleSalmonella Type III secretion injectisome
Map dataSalmonella injectisome
Sample
  • Complex: Injectisome
    • Protein or peptide: Injectisome
Biological speciesSalmonella (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 17.0 Å
AuthorsHu B / Liu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107629 United States
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 envelope- ...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.
History
DepositionJan 4, 2017-
Header (metadata) releaseFeb 8, 2017-
Map releaseMar 29, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.53
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.53
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8544.png

Downloads & links

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Map

FileDownload / File: emd_8544.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSalmonella injectisome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 400 pix.
= 1040. Å		2.6 Å/pix.
x 400 pix.
= 1040. Å		2.6 Å/pix.
x 400 pix.
= 1040. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.53 / Movie #1: 2.53
Minimum - Maximum-11.2337055 - 25.83288
Average (Standard dev.)0.00000000167 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 1040.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z1040.0001040.0001040.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-11.23425.8330.000

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Supplemental data

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Sample components

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Entire : Injectisome

EntireName: Injectisome
Components
  • Complex: Injectisome
    • Protein or peptide: Injectisome

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Supramolecule #1: Injectisome

SupramoleculeName: Injectisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella (bacteria)
Molecular weightTheoretical: 10 MDa

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Macromolecule #1: Injectisome

MacromoleculeName: Injectisome / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
SequenceString:
N

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DARK FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 5274
ExtractionNumber tomograms: 1470 / Number images used: 5274 / Software - Name: IMOD
Final angle assignmentType: NOT APPLICABLE / Software - Name: i3

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