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- EMDB-20561: Pod structure of Shigella T3SS -

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Basic information

Entry
Database: EMDB / ID: EMD-20561
TitlePod structure of Shigella T3SS
Map data
Sample
  • Complex: Pos structure of Shigella flexneri type III secretion system
Biological speciesShigella flexneri (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 18.0 Å
AuthorsLiu J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesNIAID R01 AI123351 United States
National Institutes of Health/National Institute of General Medical SciencesNIGMS P30 GM110761 United States
CitationJournal: J Biol Chem / Year: 2019
Title: The cytoplasmic domain of MxiG interacts with MxiK and directs assembly of the sorting platform in the type III secretion system.
Authors: Shoichi Tachiyama / Yunjie Chang / Meenakumari Muthuramalingam / Bo Hu / Michael L Barta / Wendy L Picking / Jun Liu / William D Picking /
Abstract: Many Gram-negative bacteria use type III secretion systems (T3SSs) to inject virulence effector proteins into eukaryotic cells. The T3SS apparatus (T3SA) is structurally conserved among diverse ...Many Gram-negative bacteria use type III secretion systems (T3SSs) to inject virulence effector proteins into eukaryotic cells. The T3SS apparatus (T3SA) is structurally conserved among diverse bacterial pathogens and consists of a cytoplasmic sorting platform, an envelope-spanning basal body, and an extracellular needle with tip complex. The sorting platform is essential for effector recognition and powering secretion. Studies using bacterial "minicells" have revealed an unprecedented level of structural detail of the sorting platform; however, many of the structure-function relationships within this complex remain enigmatic. Here, we report on improved cryo-electron tomographic approaches to enhance the resolution of the T3SA sorting platform (at ≤2 nm resolution) done in concert with biochemical and genetic methods to define the sorting platform interactome and interactions with the T3SA inner membrane ring (IR). We observed that the sorting platform consists of "pods" with 6-fold symmetry that interact with the Spa47 ATPase via radial extensions comprising MxiN. Most importantly, MxiK maintained an interaction with the IR via specific interactions with the cytoplasmic domain of the IR protein MxiG (MxiG), which is a noncanonical forkhead-associated domain, and MxiK has an elongated structure that interacts with the IR via MxiG T4 lysozyme-mediated insertional mutagenesis of MxiK revealed its orientation within the sorting platform and enabled disruption of interactions with its binding partners, which abolished sorting platform assembly. Finally, a comparison with the homologous interactions in the T3SS sorting platform revealed clear differences in their IR-sorting platform interfaces that have possible mechanistic implications.
History
DepositionAug 6, 2019-
Header (metadata) releaseNov 6, 2019-
Map releaseNov 6, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20561.png

Downloads & links

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Map

FileDownload / File: emd_20561.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.6 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.18442513 - 0.32694602
Average (Standard dev.)0.00070833997 (±0.024923632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 467.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z468.000468.000468.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1840.3270.001

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Supplemental data

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Sample components

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Entire : Pos structure of Shigella flexneri type III secretion system

EntireName: Pos structure of Shigella flexneri type III secretion system
Components
  • Complex: Pos structure of Shigella flexneri type III secretion system

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Supramolecule #1: Pos structure of Shigella flexneri type III secretion system

SupramoleculeName: Pos structure of Shigella flexneri type III secretion system
type: complex / ID: 1 / Parent: 0 / Details: wild type
Source (natural)Organism: Shigella flexneri (bacteria) / Strain: SF5a

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridMaterial: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 4488
ExtractionNumber tomograms: 922 / Number images used: 4488
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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