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- EMDB-23440: Shigella Pod -

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Basic information

Entry
Database: EMDB / ID: EMD-23440
TitleShigella Pod
Map datapod monomer, MxiG, MxiK, and Spa33
Sample
  • Organelle or cellular component: Pods of the Sorting Platform in the Shigella Type III Secretion System
Function / homology
Function and homology information


protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
Type III secretion system outer membrane, SpaO / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal ...Type III secretion system outer membrane, SpaO / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Surface presentation of antigens protein SpaO / Protein MxiG / Lipoprotein MxiJ
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsLiu J / Tachiyama S / Carroll BL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Cell Infect Microbiol / Year: 2021
Title: Composition and Biophysical Properties of the Sorting Platform Pods in the Type III Secretion System.
Authors: Shoichi Tachiyama / Ryan Skaar / Yunjie Chang / Brittany L Carroll / Meenakumari Muthuramalingam / Sean K Whittier / Michael L Barta / Wendy L Picking / Jun Liu / William D Picking /
Abstract: , causative agent of bacillary dysentery (shigellosis), uses a type III secretion system (T3SS) as its primary virulence factor. The T3SS injectisome delivers effector proteins into host cells to ..., causative agent of bacillary dysentery (shigellosis), uses a type III secretion system (T3SS) as its primary virulence factor. The T3SS injectisome delivers effector proteins into host cells to promote entry and create an important intracellular niche. The injectisome's cytoplasmic sorting platform (SP) is a critical assembly that contributes to substrate selection and energizing secretion. The SP consists of oligomeric Spa33 "pods" that associate with the basal body MxiK and connect to the Spa47 ATPase MxiN. The pods contain heterotrimers of Spa33 with one full-length copy associated with two copies of a C-terminal domain (Spa33). The structure of Spa33 is known, but the precise makeup and structure of the pods remains elusive. We show here that recombinant wild-type Spa33 can be prepared as a heterotrimer that forms distinct stable complexes with MxiK and MxiN. In two-hybrid analyses, association of the Spa33 complex with these proteins occurs the full-length Spa33 component. Furthermore, these complexes each have distinct biophysical properties. Based on these properties, new high-resolution cryo-electron tomography data and architectural similarities between the Spa33 and flagellar FliM-FliN complexes, we provide a preliminary model of the Spa33 heterotrimers within the SP pods. From these findings and evolving models of SP interfaces and dynamics in the and T3SS, we suggest a model for SP function in which two distinct complexes come together within the context of the SP to contribute to form the complete pod structures during the recruitment of T3SS secretion substrates.
History
DepositionFeb 5, 2021-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0514
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0514
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23440.png

Downloads & links

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Map

FileDownload / File: emd_23440.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpod monomer, MxiG, MxiK, and Spa33
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 160 pix.
= 400. Å		2.5 Å/pix.
x 160 pix.
= 400. Å		2.5 Å/pix.
x 160 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0514 / Movie #1: 0.0514
Minimum - Maximum-0.44775695 - 0.47378162
Average (Standard dev.)-2.7728988e-11 (±0.01682579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-0.4480.474-0.000

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Supplemental data

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Sample components

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Entire : Pods of the Sorting Platform in the Shigella Type III Secretion System

EntireName: Pods of the Sorting Platform in the Shigella Type III Secretion System
Components
  • Organelle or cellular component: Pods of the Sorting Platform in the Shigella Type III Secretion System

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Supramolecule #1: Pods of the Sorting Platform in the Shigella Type III Secretion System

SupramoleculeName: Pods of the Sorting Platform in the Shigella Type III Secretion System
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Shigella flexneri (bacteria)

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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: 7.2
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: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Details: update resolution / Number subtomograms used: 4488
ExtractionNumber tomograms: 922 / Number images used: 4488
Final angle assignmentType: NOT APPLICABLE

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