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- PDB-6ogd: Cryo-EM structure of YenTcA in its prepore state -

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Basic information

Entry
Database: PDB / ID: 6ogd
TitleCryo-EM structure of YenTcA in its prepore state
Components
  • Chitinase 2
  • Toxin subunit YenA1
  • Toxin subunit YenA2
KeywordsTOXIN / Membrane protein Pore-forming toxin Complex
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
ABC toxin, N-terminal domain / ABC toxin N-terminal region / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain / : / Chitinase insertion domain superfamily ...ABC toxin, N-terminal domain / ABC toxin N-terminal region / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Toxin subunit YenA1 / Toxin subunit YenA2 / Chitinase 2
Similarity search - Component
Biological speciesYersinia entomophaga (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPiper, S.J. / Brillault, L. / Box, J.K. / Landsberg, M.J.
Funding support Australia, New Zealand, 4items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP170104484 Australia
Australian Research Council (ARC)DP160101018 Australia
Royal Society of New Zealand14-UOA-146 New Zealand
Foundation for Science and TechnologyC10X0804 New Zealand
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 ...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.
History
DepositionApr 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Toxin subunit YenA1
B: Toxin subunit YenA2
C: Chitinase 2
D: Toxin subunit YenA1
E: Toxin subunit YenA2
F: Chitinase 2
G: Toxin subunit YenA1
H: Toxin subunit YenA2
I: Chitinase 2
J: Toxin subunit YenA1
K: Toxin subunit YenA2
L: Chitinase 2
M: Toxin subunit YenA1
N: Toxin subunit YenA2
O: Chitinase 2


Theoretical massNumber of molelcules
Total (without water)1,779,88915
Polymers1,779,88915
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Toxin subunit YenA1


Mass: 129912.320 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A877
#2: Protein
Toxin subunit YenA2


Mass: 156324.938 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A878
#3: Protein
Chitinase 2


Mass: 69740.609 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A879, chitinase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.08 MDa
Source (natural)Organism: Yersinia entomophaga (bacteria) / Strain: MH96
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2.2particle selectionparticle picking was done in e2boxer.py using the SWARM algorithm
4EMAN2.2CTF correctione2ctf.py was used to estiamte the CTF. CTF correction was performed as part of the e2refine.py routine
10EMAN2.2initial Euler assignment
11EMAN2.2final Euler assignment
13EMAN2.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 19713
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9856 / Symmetry type: POINT

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