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- EMDB-8096: The Architecture of the Cytoplasmic Region of Type III Secretion ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8096
TitleThe Architecture of the Cytoplasmic Region of Type III Secretion SystemsType three secretion system
Map dataNone
Sample
  • Complex: The needle complex of Shigella flexneri
Biological speciesShigella flexneri (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 Å
AuthorsMakino F / Shen D / Kajimura N / Kawamoto A / Pissaridou P / Oswin H / Pain M / Murillo I / Namba K / Blocker AJ
CitationJournal: Sci Rep / Year: 2016
Title: The Architecture of the Cytoplasmic Region of Type III Secretion Systems.
Authors: Fumiaki Makino / Dakang Shen / Naoko Kajimura / Akihiro Kawamoto / Panayiota Pissaridou / Henry Oswin / Maria Pain / Isabel Murillo / Keiichi Namba / Ariel J Blocker /
Abstract: Type III secretion systems (T3SSs) are essential devices in the virulence of many Gram-negative bacterial pathogens. They mediate injection of protein effectors of virulence from bacteria into ...Type III secretion systems (T3SSs) are essential devices in the virulence of many Gram-negative bacterial pathogens. They mediate injection of protein effectors of virulence from bacteria into eukaryotic host cells to manipulate them during infection. T3SSs involved in virulence (vT3SSs) are evolutionarily related to bacterial flagellar protein export apparatuses (fT3SSs), which are essential for flagellar assembly and cell motility. The structure of the external and transmembrane parts of both fT3SS and vT3SS is increasingly well-defined. However, the arrangement of their cytoplasmic and inner membrane export apparatuses is much less clear. Here we compare the architecture of the cytoplasmic regions of the vT3SSs of Shigella flexneri and the vT3SS and fT3SS of Salmonella enterica serovar Typhimurium at ~5 and ~4 nm resolution using electron cryotomography and subtomogram averaging. We show that the cytoplasmic regions of vT3SSs display conserved six-fold symmetric features including pods, linkers and an ATPase complex, while fT3SSs probably only display six-fold symmetry in their ATPase region. We also identify other morphological differences between vT3SSs and fT3SSs, such as relative disposition of their inner membrane-attached export platform, C-ring/pods and ATPase complex. Finally, using classification, we find that both types of apparatuses can loose elements of their cytoplasmic region, which may therefore be dynamic.
History
DepositionJul 18, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseOct 12, 2016-
UpdateOct 12, 2016-
Current statusOct 12, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8096.png

Downloads & links

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Map

FileDownload / File: emd_8096.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.7 Å/pix.
x 100 pix.
= 570. Å		5.7 Å/pix.
x 100 pix.
= 570. Å		5.7 Å/pix.
x 100 pix.
= 570. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-3.7672849 - 8.89988
Average (Standard dev.)0.14306465 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 570.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.75.75.7
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z570.000570.000570.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-25-77-48
NX/NY/NZ899896
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-3.7678.9000.143

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Supplemental data

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Sample components

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Entire : The needle complex of Shigella flexneri

EntireName: The needle complex of Shigella flexneri
Components
  • Complex: The needle complex of Shigella flexneri

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Supramolecule #1: The needle complex of Shigella flexneri

SupramoleculeName: The needle complex of Shigella flexneri / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Shigella flexneri (bacteria)
Recombinant expressionOrganism: Shigella flexneri (bacteria) / Recombinant strain: WT for minicells / Recombinant plasmid: pBAD24 Salmonella ftsZ

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R0.6/1.0 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49030 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 100 / Number images used: 265 / Method: manual / Software - Name: IMOD
CTF correctionSoftware - Name: TOMOCTF
Final 3D classificationNumber classes: 4 / Avg.num./class: 70 / Software - Name: Dynamo
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: Dynamo
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 265

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