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- EMDB-8544: Salmonella Type III secretion injectisome -

Open data

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Basic information

Database: EMDB / ID: 8544
TitleSalmonella Type III secretion injectisome
SourceSalmonella / bacteria
Map dataSalmonella injectisome
Methodsubtomogram averaging, at 17 Å resolution
AuthorsHu B / Liu J
CitationCell, 2017, 168, 1065-1074.e10

Cell, 2017, 168, 1065-1074.e10 StrPapers
In Situ Molecular Architecture of the Salmonella Type III Secretion Machine.
Bo Hu / Maria Lara-Tejero / Qingke Kong / Jorge E Galán / Jun Liu

DateDeposition: Jan 4, 2017 / Header (metadata) release: Feb 8, 2017 / Map release: Mar 29, 2017 / Last update: Mar 29, 2017

Structure visualization

  • 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
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8544.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
2.6 Å/pix.
= 1040. Å
400 pix
2.6 Å/pix.
= 1040. Å
400 pix
2.6 Å/pix.
= 1040. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.6 Å
Contour Level:2.53 (by author), 2.53 (movie #1):
Minimum - Maximum-11.2337055 - 25.83288
Average (Standard dev.)1.669537E-9 (1)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1040 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-200-200-200
D min/max/mean-11.23425.8330.000

Supplemental data

Sample components

Entire Injectisome

EntireName: Injectisome / Number of components: 2
MassTheoretical: 10 MDa

Component #1: protein, Injectisome

ProteinName: Injectisome / Recombinant expression: No
MassTheoretical: 10 MDa
SourceSpecies: Salmonella / bacteria

Component #2: protein, Injectisome

ProteinName: Injectisome / Recombinant expression: No

Experimental details

Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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 / Tilt Angle: -51 - 51 deg.
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 17 Å / Resolution method: FSC 0.5 CUT-OFF

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