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- PDB-7oag: Cryo-EM structure of the plectasin fibril (single strand) -

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Basic information

Entry
Database: PDB / ID: 7oag
TitleCryo-EM structure of the plectasin fibril (single strand)
ComponentsFungal defensin plectasin
KeywordsANTIMICROBIAL PROTEIN / fibril / helical
Function / homology
Function and homology information


potassium channel regulator activity / toxin activity / defense response to bacterium / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily
Similarity search - Domain/homology
Fungal defensin plectasin
Similarity search - Component
Biological speciesPseudoplectania nigrella (fungus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsEffantin, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)675074European Union
CitationJournal: Nat Commun / Year: 2022
Title: pH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils.
Authors: Christin Pohl / Gregory Effantin / Eaazhisai Kandiah / Sebastian Meier / Guanghong Zeng / Werner Streicher / Dorotea Raventos Segura / Per H Mygind / Dorthe Sandvang / Line Anker Nielsen / ...Authors: Christin Pohl / Gregory Effantin / Eaazhisai Kandiah / Sebastian Meier / Guanghong Zeng / Werner Streicher / Dorotea Raventos Segura / Per H Mygind / Dorthe Sandvang / Line Anker Nielsen / Günther H J Peters / Guy Schoehn / Christoph Mueller-Dieckmann / Allan Noergaard / Pernille Harris /
Abstract: Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of ...Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominantly β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembles into helical non-amyloid fibrils. The in vitro anti-microbial activity was determined and shown to be enhanced compared to the wildtype. Plectasin contains a cysteine-stabilised α-helix-β-sheet structure, which remains intact upon fibril formation. Two protofilaments form a right-handed protein fibril. The fibril formation is reversible and follows sigmoidal kinetics with a pH- and concentration dependent equilibrium between soluble monomer and protein fibril. This high-resolution structure reveals that α/β proteins can natively assemble into fibrils.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.0Apr 27, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Apr 27, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 27, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
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Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
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Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fungal defensin plectasin
B: Fungal defensin plectasin
C: Fungal defensin plectasin
D: Fungal defensin plectasin
E: Fungal defensin plectasin
F: Fungal defensin plectasin
G: Fungal defensin plectasin
H: Fungal defensin plectasin
I: Fungal defensin plectasin
J: Fungal defensin plectasin
K: Fungal defensin plectasin
L: Fungal defensin plectasin
M: Fungal defensin plectasin
N: Fungal defensin plectasin
O: Fungal defensin plectasin
P: Fungal defensin plectasin
Q: Fungal defensin plectasin
R: Fungal defensin plectasin
S: Fungal defensin plectasin
T: Fungal defensin plectasin
U: Fungal defensin plectasin
V: Fungal defensin plectasin
W: Fungal defensin plectasin
X: Fungal defensin plectasin
Y: Fungal defensin plectasin


Theoretical massNumber of molelcules
Total (without water)110,05225
Polymers110,05225
Non-polymers00
Water00
1


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

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Components

#1: Protein/peptide ...
Fungal defensin plectasin


Mass: 4402.092 Da / Num. of mol.: 25
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoplectania nigrella (fungus) / Gene: DEF / Production host: Escherichia coli (E. coli) / References: UniProt: Q53I06
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: assembly of plectasin's monomers into a protein fibril
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudoplectania nigrella (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 156.5 ° / Axial rise/subunit: 3.76 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66272 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0077825
ELECTRON MICROSCOPYf_angle_d0.59210375
ELECTRON MICROSCOPYf_dihedral_angle_d4.3011075
ELECTRON MICROSCOPYf_chiral_restr0.049850
ELECTRON MICROSCOPYf_plane_restr0.0041350

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