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- EMDB-20054: Cryo-EM structure of YenTcA in the pore state determined in liposomes -

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Basic information

Entry
Database: EMDB / ID: EMD-20054
TitleCryo-EM structure of YenTcA in the pore state determined in liposomes
Map data
SampleYersinia entomphaga toxin complex subunit A (YenTcA) in the pore form in liposomes:
YenA1 / YenA2 / Chi1 / Chi2Chi-squared distribution
SourceYersinia entomophaga (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 11 Å
AuthorsLandsberg MJ / Piper SJ
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin.
Authors: Sarah J Piper / Lou Brillault / Rosalba Rothnagel / Tristan I Croll / Joseph K Box / Irene Chassagnon / Sebastian Scherer / Kenneth N Goldie / Sandra A Jones / Femke Schepers / Lauren Hartley-Tassell / Thomas Ve / Jason N Busby / Julie E Dalziel / J Shaun Lott / Ben Hankamer / Henning Stahlberg / Mark R H Hurst / Michael J Landsberg /
Abstract: ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen ...ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen Yersinia entomophaga. Here we present cryo-EM structures of YenTcA, purified from the native source. The soluble pre-pore structure, determined at an average resolution of 4.4 Å, reveals a pentameric assembly that in contrast to other characterised ABC toxins is formed by two TcA-like proteins (YenA1 and YenA2) and decorated by two endochitinases (Chi1 and Chi2). We also identify conformational changes that accompany membrane pore formation by visualising YenTcA inserted into liposomes. A clear outward rotation of the Chi1 subunits allows for access of the protruding translocation pore to the membrane. Our results highlight structural and functional diversity within the ABC toxin subfamily, explaining how different ABC toxins are capable of recognising diverse hosts.
DateDeposition: Apr 2, 2019 / Header (metadata) release: May 1, 2019 / Map release: May 8, 2019 / Update: May 8, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20054.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 500 pix.
= 860. Å
1.72 Å/pix.
x 500 pix.
= 860. Å
1.72 Å/pix.
x 500 pix.
= 860. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.011636295 - 0.042337935
Average (Standard dev.)0.00015453523 (±0.0019856696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 860.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z860.000860.000860.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0120.0420.000

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Supplemental data

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Sample components

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Entire Yersinia entomphaga toxin complex subunit A (YenTcA) in the pore ...

EntireName: Yersinia entomphaga toxin complex subunit A (YenTcA) in the pore form in liposomes
Number of components: 5

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Component #1: protein, Yersinia entomphaga toxin complex subunit A (YenTcA) in ...

ProteinName: Yersinia entomphaga toxin complex subunit A (YenTcA) in the pore form in liposomes
Recombinant expression: No
MassTheoretical: 2.08 MDa
SourceSpecies: Yersinia entomophaga (bacteria) / Strain: MH96

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Component #2: protein, YenA1

ProteinName: YenA1 / Recombinant expression: No
SourceSpecies: Yersinia entomophaga (bacteria)

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Component #3: protein, YenA2

ProteinName: YenA2 / Recombinant expression: No
SourceSpecies: Yersinia entomophaga (bacteria)

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Component #4: protein, Chi1

ProteinName: Chi1 / Recombinant expression: No
SourceSpecies: Yersinia entomophaga (bacteria)

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Component #5: protein, Chi2

ProteinName: Chi2Chi-squared distribution / Recombinant expression: No
SourceSpecies: Yersinia entomophaga (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.2 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 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: single particle reconstruction / Applied symmetry: C5 (5 fold cyclic) / Number of projections: 5130
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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