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- EMDB-30782: The Shigella flexneri type III secretion system tip complex by cr... -

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Basic information

Entry
Database: EMDB / ID: EMD-30782
TitleThe Shigella flexneri type III secretion system tip complex by cryo-electron microscopy
Map data
Sample
  • Complex: Tip complex of the Shigella flexneri type III secretion system
Biological speciesShigella flexneri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsCheung M / Taba S / Villar-Briones A / Hall M / Shintake T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K16661 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101116 Japan
CitationJournal: To Be Published
Title: The Shigella flexneri type III secretion system tip complex by cryo-electron microscopy
Authors: Cheung M / Taba S / Villar-Briones A / Hall M / Shintake T
History
DepositionDec 9, 2020-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateDec 15, 2021-
Current statusDec 15, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.66
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30782.png

Downloads & links

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Map

FileDownload / File: emd_30782.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 200 pix.
= 452. Å		2.26 Å/pix.
x 200 pix.
= 452. Å		2.26 Å/pix.
x 200 pix.
= 452. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.66 / Movie #1: 0.66
Minimum - Maximum-0.5772572 - 4.68783
Average (Standard dev.)-0.009903508 (±0.15893869)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 452.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.262.262.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z452.000452.000452.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.5774.688-0.010

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Supplemental data

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Sample components

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Entire : Tip complex of the Shigella flexneri type III secretion system

EntireName: Tip complex of the Shigella flexneri type III secretion system
Components
  • Complex: Tip complex of the Shigella flexneri type III secretion system

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Supramolecule #1: Tip complex of the Shigella flexneri type III secretion system

SupramoleculeName: Tip complex of the Shigella flexneri type III secretion system
type: complex / ID: 1 / Parent: 0
Details: Tip complex analysed from purified needle complexes, the main structural component of the type III secretion system
Source (natural)Organism: Shigella flexneri (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Details: 150 mM NaCl, 10 mM Tris-HCl pH 8, 0.2% (w/v) n-dodecyl-B-D-maltoside
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Double-sided blotting graphene oxide grid preparation method (Cheung et al., 2018)..
DetailsNeedle complexes dispersed in vitreous ice films using the double-blotting graphene oxide procedure (Cheung et al., 2018)

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 67700
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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