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- EMDB-20315: InvG secretin domain beta-barrel from Salmonella SPI-1 injectisom... -

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Basic information

Entry
Database: EMDB / ID: EMD-20315
TitleInvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base
Map dataInvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base
Sample
  • Complex: InvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
: / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsHu J / Worrall LJ / Vuckovic M / Hong C / Atkinson CE / Yu Z / Strynadka NCJ
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research Canada
CitationJournal: Nat Microbiol / Year: 2019
Title: T3S injectisome needle complex structures in four distinct states reveal the basis of membrane coupling and assembly.
Authors: Jinhong Hu / Liam J Worrall / Marija Vuckovic / Chuan Hong / Wanyin Deng / Claire E Atkinson / B Brett Finlay / Zhiheng Yu / Natalie C J Strynadka /
Abstract: The bacterial injectisome is a syringe-shaped macromolecular nanomachine utilized by many pathogenic Gram-negative bacteria, including the causative agents of plague, typhoid fever, whooping cough, ...The bacterial injectisome is a syringe-shaped macromolecular nanomachine utilized by many pathogenic Gram-negative bacteria, including the causative agents of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. Bacterial proteins destined for self-assembly and host-cell targeting are translocated by the injectisome in a process known as type III secretion (T3S). The core structure is the ~4 MDa needle complex (NC), built on a foundation of three highly oligomerized ring-forming proteins that create a hollow scaffold spanning the bacterial inner membrane (IM) (24-mer ring-forming proteins PrgH and PrgK in the Salmonella enterica serovar Typhimurium Salmonella pathogenicity island 1 (SPI-1) type III secretion system (T3SS)) and outer membrane (OM) (15-mer InvG, a member of the broadly conserved secretin pore family). An internalized helical needle projects from the NC and bacterium, ultimately forming a continuous passage to the host, for delivery of virulence effectors. Here, we have captured snapshots of the entire prototypical SPI-1 NC in four distinct needle assembly states, including near-atomic resolution, and local reconstructions in the absence and presence of the needle. These structures reveal the precise localization and molecular interactions of the internalized SpaPQR 'export apparatus' complex, which is intimately encapsulated and stabilized within the IM rings in the manner of a nanodisc, and to which the PrgJ rod directly binds and functions as an initiator and anchor of needle polymerization. We also describe the molecular details of the extensive and continuous coupling interface between the OM secretin and IM rings, which is remarkably facilitated by a localized 16-mer stoichiometry in the periplasmic-most coupling domain of the otherwise 15-mer InvG oligomer.
History
DepositionJun 19, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseOct 23, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pee
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6pee
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_20315.png

Downloads & links

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Map

FileDownload / File: emd_20315.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 250 pix.
= 427.5 Å		1.71 Å/pix.
x 250 pix.
= 427.5 Å		1.71 Å/pix.
x 250 pix.
= 427.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.13932115 - 0.28144988
Average (Standard dev.)0.00032320622 (±0.0056712343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 427.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z427.500427.500427.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.1390.2810.000

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Supplemental data

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Sample components

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Entire : InvG secretin domain beta-barrel from Salmonella SPI-1 injectisom...

EntireName: InvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base
Components
  • Complex: InvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base

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Supramolecule #1: InvG secretin domain beta-barrel from Salmonella SPI-1 injectisom...

SupramoleculeName: InvG secretin domain beta-barrel from Salmonella SPI-1 injectisome NC-base
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Molecular weightTheoretical: 4 MDa

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185855
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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