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- EMDB-54430: Lectin/toxin 2 from Coprinopsis cinerea -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54430
TitleLectin/toxin 2 from Coprinopsis cinerea
Map data
Sample
  • Complex: monomeric coprinopsis cinerea toxin 2
    • Protein or peptide: Ricin B lectin domain-containing protein
Keywordsfungal lectin / toxin / 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 (fungus) / Coprinopsis cinerea okayama7#130 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsCordara G / Ali Ahmad A / Krengel U
Funding support Norway, Switzerland, 2 items
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 SS / Cordara G / Kersten F / Steiner K / Samin CH / Plaza DF / Ahmad AA / Boeggild A / Karlsen JL / Sokolowska BO / Boesen T / Krengel U / Kunzler M
History
DepositionJul 17, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54430.png

Downloads & links

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Map

FileDownload / File: emd_54430.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.52341217 - 1.6789333
Average (Standard dev.)-0.000073152885 (±0.03439982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 302.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54430_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54430_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54430_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : monomeric coprinopsis cinerea toxin 2

EntireName: monomeric coprinopsis cinerea toxin 2
Components
  • Complex: monomeric coprinopsis cinerea toxin 2
    • Protein or peptide: Ricin B lectin domain-containing protein

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Supramolecule #1: monomeric coprinopsis cinerea toxin 2

SupramoleculeName: monomeric coprinopsis cinerea toxin 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Coprinopsis cinerea (fungus) / Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003
Molecular weightTheoretical: 90.9 kDa/nm

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Macromolecule #1: Ricin B lectin domain-containing protein

MacromoleculeName: Ricin B lectin domain-containing protein / type: protein_or_peptide / ID: 1
Details: N-terminal 6xHis-tag, followed by TEVp cleavage site
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coprinopsis cinerea okayama7#130 (fungus) / Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003
Molecular weightTheoretical: 91.040594 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MHHHHHHHHE NLYFQSMALN EGVYWIRNSR FTNKVLDLDA ANVAKGTSIL DFNEHGTFNE NHNQLWIVER FQSRDTYLIR SVHSNLVLD LSQGLSANGT PILCWTQHGG TNQQWRIEWV KDDNKTPLYR IVSVATGTAI SHNEDDSSAY TVAWSVDDGP K QLWSFDPF ...String:
MHHHHHHHHE NLYFQSMALN EGVYWIRNSR FTNKVLDLDA ANVAKGTSIL DFNEHGTFNE NHNQLWIVER FQSRDTYLIR SVHSNLVLD LSQGLSANGT PILCWTQHGG TNQQWRIEWV KDDNKTPLYR IVSVATGTAI SHNEDDSSAY TVAWSVDDGP K QLWSFDPF VTPLLYRLRV KSTSRVLDLA AASADNGTLA LAWEQHTAIT KRNQLWWLPY RSGAEEYTIQ CLETSTVADL SG GNSGNGT PIYGWQSHGG RNQQWKFEPT SDSGDYYHIK NVEGGSVMDA YMNDSQKRVG GWSNNGGDNQ KWLLDPLPSP GPG WVLIQN GGTGKFLCST PSGDIGTADG PETVYDYSVQ WRFIQREYTG VYHVVNRATG AYLRQIGTSM PSIGLAEEND DELK DWWML ETYDNSEIGL ASIISRWTGN VLDHYGGVSV QALDNNTENS YRSWAIIPAR DWLTSFSLVN GQGGLCLAAQ YAREE TRLS TTANVNDFHA QWVFRKPSGS SGYTIQNKYN NHYVGGTSAR WELVVCCNKY FGIRNTSTQK YLAIEDGQVT FQDQDM TDR KQCWELCSGR ATDTSGNDYD LIYMDDDLLE VMIPWVGDKQ GDLKHYIEKR ATKKPPKDKG GWQLPAAGLI KKPKFND IR QLLQELIEQW EWDVVNEERE QIQTLVSIDE AEARRLLGRR PHPDIVAAYQ RSRSSTLFRI DRQGYFNIAG DRYVNIQG Q YGDDSYFHIA LPVGVRFGRE QIRRFLRDSL DRSTSVTITP TTCKPPSGGP DYNRDPDSDG DNSWIKWTIA VVGTSAIKH SEL

UniProtKB: Ricin B lectin domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Component - Concentration: 20.0 mM / Component - Formula: C8H18N2O4S
Component - Name: HEPES (2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid)
Details: 20 mM HEPES, pH 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: Instrument: Pelco EasyGlow Settings: 30s at 15 uA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Plunge-freezing: Blot time: 5s Blot force: -5 Wait time: 1s Drain time: 0s Sample volume: 4 ul.
Detailsthe sample was purified by SEC, and stored at 4 degree Celsius until grid preparation

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Number grids imaged: 1 / Number real images: 7500 / Average exposure time: 5.0 sec. / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 215000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5928015
CTF correctionSoftware - Name: cryoSPARC (ver. 3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 204524
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: RoseTTAFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 63.4 / Target criteria: real-space correlation coefficient
Output model

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

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