+Open data
-Basic information
Entry | Database: PDB / ID: 7oag | ||||||
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Title | Cryo-EM structure of the plectasin fibril (single strand) | ||||||
Components | Fungal defensin plectasin | ||||||
Keywords | ANTIMICROBIAL 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 | ||||||
Biological species | Pseudoplectania nigrella (fungus) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Effantin, G. | ||||||
Funding support | European Union, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oag.cif.gz | 163.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oag.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 7oag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oag_validation.pdf.gz | 859.9 KB | Display | wwPDB validaton report |
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Full document | 7oag_full_validation.pdf.gz | 864 KB | Display | |
Data in XML | 7oag_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 7oag_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/7oag ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oag | HTTPS FTP |
-Related structure data
Related structure data | 12776MC 7o76C 7oaeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein/peptide | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: assembly of plectasin's monomers into a protein fibril Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Pseudoplectania nigrella (fungus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 5.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 156.5 ° / Axial rise/subunit: 3.76 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66272 / Symmetry type: HELICAL | ||||||||||||||||||||||||
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