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- PDB-9s11: Lectin/toxin 2 from Coprinopsis cinerea -

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Basic information

Entry
Database: PDB / ID: 9s11
TitleLectin/toxin 2 from Coprinopsis cinerea
ComponentsRicin B lectin domain-containing protein
KeywordsTOXIN / fungal lectin / chimerolectin / nematotoxin
Function / homologyRicin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Ricin B lectin domain-containing protein
Function and homology information
Biological speciesCoprinopsis cinerea okayama7#130 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsCordara, G. / Krengel, U.
Funding support Norway, Switzerland, 2items
OrganizationGrant numberCountry
Norwegian Research Council245828 Norway
Swiss National Science Foundation31003A-130671 Switzerland
Citation
Journal: EMBO J / Year: 2026
Title: Structure and function of a fungal AB toxin-like chimerolectin involved in anti-nematode defense.
Authors: Stefanie S Schmieder / Gabriele Cordara / Flore Kersten / Kevin Steiner / Clara H Samim / David F Plaza / Ahmad Ali-Ahmad / Andreas Boeggild / Jesper L Karlsen / Blanka O Sokolowska / Thomas ...Authors: Stefanie S Schmieder / Gabriele Cordara / Flore Kersten / Kevin Steiner / Clara H Samim / David F Plaza / Ahmad Ali-Ahmad / Andreas Boeggild / Jesper L Karlsen / Blanka O Sokolowska / Thomas Boesen / Ute Krengel / Markus Künzler /
Abstract: Fungal defense against predators largely relies on protein toxins, many of which are lectins. We previously showed that the production of the nematotoxin CCTX2 is upregulated in the Agaricomycete ...Fungal defense against predators largely relies on protein toxins, many of which are lectins. We previously showed that the production of the nematotoxin CCTX2 is upregulated in the Agaricomycete Coprinopsis cinerea upon predation by nematodes. Here, we classify CCTX2 as the founding member of a previously unknown family of fungal chimerolectins. Cryo-EM analysis to 3.2 Å resolution reveals five domains, with the four N-terminal β-trefoil fold (BTF) domains cradling a C-terminal domain, which exhibits an unusual α + β protein fold with some similarity to killer protein 4. Mutational analysis suggests that both terminal domains are functionally required for nematotoxicity. The first two BTF domains enable CCTX2 binding to glycosphingolipids with LacNAc or LacdiNAc glycoepitopes on nematode intestinal epithelial cells, whereas the biochemical function of the C-terminal domain remains unknown. Experiments in the model nematode Caenorhabditis elegans demonstrate that CCTX2 exploits the endocytic and retrograde trafficking machinery of cells in the intestinal epithelium to exert its toxicity and access the yet-to-be-identified intracellular target of the non-lectin domain. Our findings thus show that the molecular architecture and mode of action of CCTX2 is reminiscent of bacterial and plant AB toxins.
#1: Journal: Biorxiv / Year: 2025
Title: Structure and function of a fungal AB toxin-like chimerolectin involved in anti-nematode defense
Authors: Schmieder, S.S. / Cordara, G. / Kersten, F. / Steiner, K. / Samin, C.H. / Plaza, D.F. / Ahmad, A.A. / Boeggild, A. / Karlsen, J.L. / Sokolowska, B.O. / Boesen, T. / Krengel, U. / Kunzler, M.
History
DepositionJul 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.1Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin B lectin domain-containing protein


Theoretical massNumber of molelcules
Total (without water)91,0411
Polymers91,0411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ricin B lectin domain-containing protein


Mass: 91040.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 6xHis-tag, followed by TEVp cleavage site
Source: (gene. exp.) Coprinopsis cinerea okayama7#130 (fungus)
Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003 / Gene: CC1G_10077 / Details (production host): pET-22b(+) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A8NDT7
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: monomeric coprinopsis cinerea toxin 2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 90.9 kDa/nm / Experimental value: NO
Source (natural)Organism: Coprinopsis cinerea (fungus) / Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003
Source (recombinant)Organism: Escherichia coli K-12 (bacteria) / Strain: C41 / Plasmid: pET-22b(+)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES, pH 7.5
Buffer componentConc.: 20 mM
Name: HEPES (2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid)
Formula: C8H18N2O4S
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: the sample was purified by SEC, and stored at 4 degree Celsius until grid preparation
Specimen supportDetails: Instrument: Pelco EasyGlow Settings: 30s at 15 uA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Plunge-freezing: Blot time: 5s Blot force: -5 Wait time: 1s Drain time: 0s Sample volume: 4 ul

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingAverage exposure time: 5 sec. / Electron dose: 59.5 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7500

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.1particle selection
2EPU2.11.0image acquisition
4cryoSPARC3.1CTF correction
7Coot0.9.8.96model fitting
9PHENIX1.21.2-5419model refinement
10cryoSPARC3.1initial Euler assignment
11cryoSPARC3.1final Euler assignment
12cryoSPARC3.1classification
13cryoSPARC3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5928015
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204524 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 63.4 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: real-space correlation coefficient
Atomic model buildingSource name: RoseTTAFold / Type: in silico model
RefinementHighest resolution: 3.16 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056435
ELECTRON MICROSCOPYf_angle_d0.8228758
ELECTRON MICROSCOPYf_dihedral_angle_d8.205876
ELECTRON MICROSCOPYf_chiral_restr0.049922
ELECTRON MICROSCOPYf_plane_restr0.0051148

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