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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
CitationJournal: 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

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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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