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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 injectisome
SampleSpaO mutant of Salmonella injectisome
SourceSalmonella / bacteria
Map dataSpaO mutant structure of Salmonella Type III secretion injectisome
Methodsubtomogram averaging, at 30 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: Jan 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.98
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.98
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

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

Image control

Size
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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 package.

Voxel sizeX=Y=Z: 5.2 Å
Density
Contour Level:1.98 (by author), 1.98 (movie #1):
Minimum - Maximum-12.461525 - 13.407977
Average (Standard dev.)-1.29946E-10 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 1040 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
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

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

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 30 Å / Resolution method: FSC 0.5 CUT-OFF

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