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- PDB-9kl3: CryoEM structure of Pleurocybella porrigens lectin (PPL) in compl... -

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Basic information

Entry
Database: PDB / ID: 9kl3
TitleCryoEM structure of Pleurocybella porrigens lectin (PPL) in complex with GalNAc
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / trefoil / lectin
Function / homologyRicin-type beta-trefoil lectin domain-like / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / 2-acetamido-2-deoxy-alpha-D-galactopyranose / Lectin
Function and homology information
Biological speciesPleurocybella porrigens (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsIshimoto, N. / Adachi, D. / Kawabata, H. / Park, S.Y. / Tame, J.R.H. / Kamata, K.
Funding support1items
OrganizationGrant numberCountry
Other privateY-2023-2-046
CitationJournal: Glycobiology / Year: 2025
Title: Crystal and Cryo-EM structure of PPL, a novel hexameric R-type lectin from the poisonous mushroom Pleurocybella porrigens.
Authors: Daisuke Adachi / Naito Ishimoto / Kenji Mizutani / Katsuya Takahashi / Reiji Kubota / Haruka Kawabata / Sam-Yong Park / Laurens Vandebroek / Arnout R D Voet / Masao Yamada / Yasuhiro Ozeki / ...Authors: Daisuke Adachi / Naito Ishimoto / Kenji Mizutani / Katsuya Takahashi / Reiji Kubota / Haruka Kawabata / Sam-Yong Park / Laurens Vandebroek / Arnout R D Voet / Masao Yamada / Yasuhiro Ozeki / Yuki Fujii / Hideaki Fujita / Jeremy R H Tame / Kenichi Kamata /
Abstract: Pleurocybella porrigens is a mushroom that grows widely around the temperate northern hemisphere, and was once considered edible, especially in Japan. Following a number of deaths in 2004, ...Pleurocybella porrigens is a mushroom that grows widely around the temperate northern hemisphere, and was once considered edible, especially in Japan. Following a number of deaths in 2004, investigations revealed the presence of various toxins, including a lectin (PPL) that apparently survives cooking and enters the bloodstream via the stomach. We have cloned PPL and solved its structure by X-ray crystallography and cryo-EM. We report the sugar binding properties of this β-trefoil lectin, which has a novel hexameric structure.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8462
Polymers14,6251
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, AUC
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Lectin


Mass: 14625.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurocybella porrigens (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: B6ZK51
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: Pleurocybella porrigens lectin in complex with GalNac / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.0856 MDa / Experimental value: YES
Source (natural)Organism: Pleurocybella porrigens (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.8 sec. / Electron dose: 47.41 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1542

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Processing

EM software
IDNameCategory
1Topazparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
20PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 150096
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74285 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026282
ELECTRON MICROSCOPYf_angle_d0.4078616
ELECTRON MICROSCOPYf_dihedral_angle_d3.593876
ELECTRON MICROSCOPYf_chiral_restr0.0421020
ELECTRON MICROSCOPYf_plane_restr0.0061122

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