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- PDB-9c4k: Yersinia entomophaga holotoxin complex in prepore conformation -

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Basic information

Entry
Database: PDB / ID: 9c4k
TitleYersinia entomophaga holotoxin complex in prepore conformation
Components
  • Chitinase 2
  • Toxin subunit YenA1
  • Toxin subunit YenA2
  • Toxin subunit YenB
  • Toxin subunit YenC2
KeywordsTOXIN / pore-forming / insecticidal / chitinases
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region / cytoplasm
Similarity search - Function
YwqJ-like deaminase / YwqJ-like deaminase / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat ...YwqJ-like deaminase / YwqJ-like deaminase / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / 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 / Regulator of chromosome condensation (RCC1) signature 2. / Rhs repeat-associated core / : / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Integrin alpha, N-terminal / 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 / Toxin subunit YenB / Toxin subunit YenC2
Similarity search - Component
Biological speciesYersinia entomophaga (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLow, Y.S. / Landsberg, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220101681 Australia
Australian Research Council (ARC)DP170104484 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins.
Authors: Yu Shang Low / Solace G Roche / Nadezhda A Aleksandrova / Gabriel Foley / Jason Kk Low / Joseph K Box / Tristan I Croll / Irene R Chassagnon / J Shaun Lott / Evelyne Deplazes / Mikael Bodén ...Authors: Yu Shang Low / Solace G Roche / Nadezhda A Aleksandrova / Gabriel Foley / Jason Kk Low / Joseph K Box / Tristan I Croll / Irene R Chassagnon / J Shaun Lott / Evelyne Deplazes / Mikael Bodén / Mark Rh Hurst / Sarah J Piper / Michael J Landsberg /
Abstract: ABC toxins are toxin-translocating, pore-forming proteins found in a wide range of insecticidal bacteria and some mammalian pathogens. The Yersinia entomopahaga toxin complex (YenTc) belongs to a ...ABC toxins are toxin-translocating, pore-forming proteins found in a wide range of insecticidal bacteria and some mammalian pathogens. The Yersinia entomopahaga toxin complex (YenTc) belongs to a distinct subclass of ABC toxins, defined by a divergent molecular architecture. Structural details that define their mechanism of action remain to be elucidated. Here we determine structures of the YenTc holotoxin assembly in both prepore and pore-forming configurations using cryo-EM in conjunction with Alphafold2-assisted structural modelling of flexible domains. We define the structural mechanism via which enzymatically-active chitinase subunits are incorporated, and show using phylogenetic analyses that this subclass-defining feature has evolved relatively recently. Our structures point to the existence of distinct conformational states in YenTc, which may distinguish it from other structurally-characterised ABC toxins, or represent states on a shared mechanistic trajectory. Thus, our findings enhance our understanding of the structural diversity that defines distinct ABC toxin subclasses.
History
DepositionJun 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
P: Toxin subunit YenB
Q: Toxin subunit YenC2


Theoretical massNumber of molelcules
Total (without water)2,054,60117
Polymers2,054,60117
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "D"
d_3ens_1chain "G"
d_4ens_1chain "J"
d_5ens_1chain "M"
d_1ens_2chain "H"
d_2ens_2chain "E"
d_3ens_2chain "B"
d_4ens_2chain "K"
d_5ens_2chain "N"
d_1ens_3chain "I"
d_2ens_3chain "F"
d_3ens_3chain "C"
d_4ens_3chain "L"
d_5ens_3chain "O"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1LYSLYSVALVALAA132 - 1164132 - 1164
d_2ens_1LYSLYSVALVALDD132 - 1164132 - 1164
d_3ens_1LYSLYSVALVALGG132 - 1164132 - 1164
d_4ens_1LYSLYSVALVALJJ132 - 1164132 - 1164
d_5ens_1LYSLYSVALVALMM132 - 1164132 - 1164
d_1ens_2SERSERILEILEHH2 - 13442 - 1344
d_2ens_2SERSERILEILEEE2 - 13442 - 1344
d_3ens_2SERSERILEILEBB2 - 13442 - 1344
d_4ens_2SERSERILEILEKK2 - 13442 - 1344
d_5ens_2SERSERILEILENN2 - 13442 - 1344
d_1ens_3VALVALSERSERII2 - 6322 - 632
d_2ens_3VALVALSERSERFF2 - 6322 - 632
d_3ens_3VALVALSERSERCC2 - 6322 - 632
d_4ens_3VALVALSERSERLL2 - 6322 - 632
d_5ens_3VALVALSERSEROO2 - 6322 - 632

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.308522449687, 0.951200845154, -0.00555429715522), (-0.950983636673, 0.308570832654, 0.0203510199826), (0.0210718015052, -0.000996700830829, 0.999777468124)-101.714404922, 653.396208146, -7.9884994686
2given(-0.808877255113, 0.587859855449, 0.011763354642), (-0.587313077843, -0.808752307791, 0.0313536797954), (0.0279452098864, 0.01845250643, 0.999439127837)487.958988585, 951.912497073, -18.423132954
3given(-0.80892619195, -0.587269421414, 0.0274416225744), (0.58779669831, -0.808805681545, 0.018122112362), (0.0115523778074, 0.0307895464886, 0.999459126925)954.443936644, 483.547665136, -16.7741327348
4given(0.309806272994, -0.950588049689, 0.0200607328362), (0.950782531381, 0.309858514955, -0.000527950001503), (-0.00571412592326, 0.0192369565696, 0.999798623857)652.590029463, -105.431328005, -5.33853553546
5given(0.308858197045, -0.95087647314, 0.0209892102651), (0.95109788121, 0.308881950911, -0.00218191653086), (-0.00440845511922, 0.0206366962172, 0.999777321353)652.807583611, -104.404793448, -6.47386867191
6given(-0.810093457474, -0.58559468442, 0.0287655303712), (0.586166965481, -0.809981334039, 0.0183991056147), (0.0125251242184, 0.03176639873, 0.999416838549)953.758610703, 484.635143013, -17.6321657651
7given(0.309264814234, 0.950965713285, -0.00441438936243), (-0.950736327072, 0.309287754953, 0.0210124015945), (0.0213473900455, -0.00230147614702, 0.999769469501)-102.437331626, 652.705271547, -7.61842338962
8given(-0.80839686073, 0.58851163423, 0.0121890089034), (-0.587933961515, -0.808269417697, 0.0321590626752), (0.028777985659, 0.0188309530191, 0.999408436401)487.234238237, 951.634586864, -18.973178182
9given(0.313441533189, -0.949368493631, 0.02130419142), (0.94960420349, 0.313420674741, -0.0043974263853), (-0.00250239598639, 0.0216088857926, 0.999763369037)650.43369596, -104.37102683, -7.42792149684
10given(-0.807236477823, -0.589445242113, 0.0303903837248), (0.590065620818, -0.807151978744, 0.0181175698801), (0.0138503429938, 0.0325574839362, 0.999373893114)953.301894336, 482.192275223, -18.3935660934
11given(0.306846371324, 0.951730451268, -0.00737919600101), (-0.951495776413, 0.306934622664, 0.0211405978558), (0.0223850814775, 0.00053435808862, 0.999749279864)-100.522599089, 653.682450516, -9.07372711316
12given(-0.811547717933, 0.584191756413, 0.0105020596127), (-0.583539161328, -0.811287841985, 0.0359733879906), (0.029535549994, 0.0230657578715, 0.999297564342)490.642136095, 949.266349759, -20.6075807653

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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
#4: Protein Toxin subunit YenB


Mass: 167147.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A880
#5: Protein Toxin subunit YenC2


Mass: 107563.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A882
Has protein modificationN

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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 holotoxin complex in pre-pore conformation
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7Coot0.8.9.3model fitting
8ISOLDE1.6.0model fitting
10PHENIX1.21_5207model refinement
11cryoSPARCinitial Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60315 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6OGD

6ogd


Accession code: 6OGD / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 249.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0075136834
ELECTRON MICROSCOPYf_angle_d1.0818185792
ELECTRON MICROSCOPYf_chiral_restr0.053120462
ELECTRON MICROSCOPYf_plane_restr0.009524253
ELECTRON MICROSCOPYf_dihedral_angle_d14.200450236
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints3.14230529025E-12
ens_1d_3AAELECTRON MICROSCOPYNCS constraints3.63755559701E-11
ens_1d_4AAELECTRON MICROSCOPYNCS constraints2.24126496976E-12
ens_1d_5AAELECTRON MICROSCOPYNCS constraints1.24642244917E-12
ens_2d_2HHELECTRON MICROSCOPYNCS constraints3.43685101124E-12
ens_2d_3HHELECTRON MICROSCOPYNCS constraints0.0357946678371
ens_2d_4HHELECTRON MICROSCOPYNCS constraints0.0357946678371
ens_2d_5HHELECTRON MICROSCOPYNCS constraints0.0357946678371
ens_3d_2IIELECTRON MICROSCOPYNCS constraints1.96765913937E-10
ens_3d_3IIELECTRON MICROSCOPYNCS constraints2.09960645891E-12
ens_3d_4IIELECTRON MICROSCOPYNCS constraints5.506070418E-11
ens_3d_5IIELECTRON MICROSCOPYNCS constraints2.8517820821E-12

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