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- EMDB-20053: Cryo-EM structure of YenTcA in its prepore state -

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Entry
Database: EMDB / ID: EMD-20053
TitleCryo-EM structure of YenTcA in its prepore state
Map data
SampleYersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form:
(Toxin subunit ...) x 2 / Chitinase 2
Function / homology
Function and homology information


chitinase / chitin catabolic process / chitinase activity / chitin binding / polysaccharide catabolic process / pathogenesis / extracellular region
Chitinase II / Glycoside hydrolase family 18, catalytic domain / Salmonella virulence plasmid 28.1kDa A protein / Glycosyl hydrolases family 18 / Chitinase insertion domain superfamily / Insecticidal toxin complex/plasmid virulence protein / Glycoside hydrolase superfamily
Toxin subunit YenA1 / Toxin subunit YenA2 / Chitinase 2
SourceYersinia entomophaga (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPiper SJ / Brillault L / Box JK / Landsberg MJ
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.
Validation ReportPDB-ID: 6ogd

SummaryFull reportAbout validation report
DateDeposition: Apr 2, 2019 / Header (metadata) release: May 8, 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: 7.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ogd
  • Surface level: 7.5
  • 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_20053.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 416 pix.
= 557.44 Å
1.34 Å/pix.
x 416 pix.
= 557.44 Å
1.34 Å/pix.
x 416 pix.
= 557.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 7.5 / Movie #1: 7.5
Minimum - Maximum-45.992274999999999 - 58.495677999999998
Average (Standard dev.)0.0041607455 (±1.6544155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 557.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z557.440557.440557.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-45.99258.4960.004

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Supplemental data

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Sample components

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Entire Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-...

EntireName: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form
Number of components: 4

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

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

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Component #2: protein, Toxin subunit YenA1

ProteinName: Toxin subunit YenA1 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 129.91232 kDa
SourceSpecies: Yersinia entomophaga (bacteria)

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Component #3: protein, Toxin subunit YenA2

ProteinName: Toxin subunit YenA2 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 156.324938 kDa
SourceSpecies: Yersinia entomophaga (bacteria)

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Component #4: protein, Chitinase 2

ProteinName: Chitinase 2 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 69.740609 kDa
SourceSpecies: Yersinia entomophaga (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
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: 80 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: 9856
3D reconstructionSoftware: EMAN / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

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