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- EMDB-20044: High-resolution filamentous structures of in vitro polymerized Pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-20044
TitleHigh-resolution filamentous structures of in vitro polymerized PrgI needle
Map data
SamplePrgI:
Protein PrgI
Function / homologyType III secretion system, needle protein / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / type III protein secretion system complex / protein secretion by the type III secretion system / pathogenesis / Type III secretion system apparatus
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) / Salmonella typhimurium (strain SL1344) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGuo EZ / Galan JE
CitationJournal: PLoS Biol. / Year: 2019
Title: A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion.
Authors: Emily Z Guo / Daniel C Desrosiers / Jan Zalesak / James Tolchard / Mélanie Berbon / Birgit Habenstein / Thomas Marlovits / Antoine Loquet / Jorge E Galán /
Abstract: Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines ...Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines is the injectisome, a multiprotein complex that mediates the selection of substrates, their passage through the bacterial envelope, and ultimately their delivery into eukaryotic target cells. The injectisome is composed of a large cytoplasmic complex or sorting platform, a multiring base embedded in the bacterial envelope, and a needle-like filament that protrudes several nanometers from the bacterial surface and is capped at its distal end by the tip complex. A characteristic feature of these machines is that their activity is stimulated by contact with target host cells. The sensing of target cells, thought to be mediated by the distal tip of the needle filament, generates an activating signal that must be transduced to the secretion machine by the needle filament. Here, through a multidisciplinary approach, including solid-state NMR (SSNMR) and cryo electron microscopy (cryo-EM) analyses, we have identified critical residues of the needle filament protein of a Salmonella Typhimurium type III secretion system that are involved in the regulation of the activity of the secretion machine. We found that mutations in the needle filament protein result in various specific phenotypes associated with different steps in the type III secretion process. More specifically, these studies reveal an important role for a polymorphic helix of the needle filament protein and the residues that line the lumen of its central channel in the control of type III secretion.
Validation ReportPDB-ID: 6off

SummaryFull reportAbout validation report
DateDeposition: Mar 29, 2019 / Header (metadata) release: Apr 10, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6off
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6off
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20044.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 267.52 Å
1.05 Å/pix.
x 256 pix.
= 267.52 Å
1.05 Å/pix.
x 256 pix.
= 267.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.066631444 - 0.12283311
Average (Standard dev.)0.00028913943 (±0.004262256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 267.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z267.520267.520267.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0670.1230.000

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Supplemental data

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Sample components

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Entire PrgI

EntireName: PrgI / Number of components: 2

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Component #1: protein, PrgI

ProteinName: PrgI / Recombinant expression: No
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Protein PrgI

ProteinName: Protein PrgI / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 9.147145 kDa
SourceSpecies: Salmonella typhimurium (strain SL1344) (bacteria) / Strain: SL1344
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.25 Å / Delta phi: 63.34 %deg;
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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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: 47.2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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