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- EMDB-10045: Inner membrane ring of the Shigella type 3 secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-10045
TitleInner membrane ring of the Shigella type 3 secretion system
Map data
SampleThe periplasmic inner membrane ring of the Shigella type 3 secretion system:
Protein MxiG / Lipoprotein MxiJ
Function / homology
Function and homology information


protein secretion / cell outer membrane / pathogenesis / integral component of membrane / plasma membrane
Flagellar M-ring , N-terminal / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Lipoprotein YscJ/Flagellar M-ring protein
Protein MxiG / Lipoprotein MxiJ
Biological speciesShigella flexneri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsLunelli M / Kamprad A
Funding support2 items
OrganizationGrant numberCountry
European Research Council311371
European Union653706
CitationJournal: PLoS Pathog / Year: 2020
Title: Cryo-EM structure of the Shigella type III needle complex.
Authors: Michele Lunelli / Antje Kamprad / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / Michael Kolbe /
Abstract: The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram- ...The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 6, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rwx
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rwx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10045.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 480 pix.
= 664.171 Å
1.38 Å/pix.
x 480 pix.
= 664.171 Å
1.38 Å/pix.
x 480 pix.
= 664.171 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38369 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.3866547 - 0.6354907
Average (Standard dev.)0.0004545977 (±0.011630482)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 664.1712 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.38368958333331.38368958333331.3836895833333
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z664.171664.171664.171
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.3870.6350.000

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Supplemental data

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Segmentation: #1

Fileemd_10045_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Masked C24 map of inner membrane ring of...

Fileemd_10045_additional.map
AnnotationMasked C24 map of inner membrane ring of Shigella type 3 secretion system, post-processed, sharpened (b=-128) and filtered at 3.2 A. Used for model building and refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map

Fileemd_10045_half_map_1.map
AnnotationUnfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map

Fileemd_10045_half_map_2.map
AnnotationUnfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire The periplasmic inner membrane ring of the Shigella type 3 secret...

EntireName: The periplasmic inner membrane ring of the Shigella type 3 secretion system
Details: Focused reconstruction from isolated needle complexes of the Shigella type 3 secretion system
Number of components: 3

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Component #1: protein, The periplasmic inner membrane ring of the Shigella type...

ProteinName: The periplasmic inner membrane ring of the Shigella type 3 secretion system
Details: Focused reconstruction from isolated needle complexes of the Shigella type 3 secretion system
Recombinant expression: No
SourceSpecies: Shigella flexneri (bacteria) / Strain: M90T
Source (natural)Location in cell: Membrane

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Component #2: protein, Protein MxiG

ProteinName: Protein MxiG / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 43.053844 kDa
SourceSpecies: Shigella flexneri (bacteria)

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Component #3: protein, Lipoprotein MxiJ

ProteinName: Lipoprotein MxiJ / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 27.542055 kDa
SourceSpecies: Shigella flexneri (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Drain time: 0 sec.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: OTHER
LensMagnification: 101179 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.5 - 4.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5238

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C24 (24 fold cyclic) / Number of projections: 72298
3D reconstructionSoftware: RELION / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient and geometry / Refinement space: REAL
Details: Model was built and refined in the map low-pass filtered at 3.2 A
Input PDB model: 3GR0, 2Y9J
Chain ID: D, t

Overall bvalue: 140
Output model

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