+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12775 | |||||||||
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Title | Cryo-EM structure of the plectasin fibril (double strands) | |||||||||
Map data | Plectasin double strands | |||||||||
Sample |
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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 | helical reconstruction / cryo EM / Resolution: 2.0 Å | |||||||||
Authors | Effantin G | |||||||||
Funding support | European Union, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_12775.map.gz | 78.3 MB | EMDB map data format | |
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Header (meta data) | emd-12775-v30.xml emd-12775.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12775_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_12775.png | 175.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12775 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12775 | HTTPS FTP |
-Validation report
Summary document | emd_12775_validation.pdf.gz | 459 KB | Display | EMDB validaton report |
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Full document | emd_12775_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | emd_12775_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_12775_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12775 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12775 | HTTPS FTP |
-Related structure data
Related structure data | 7oaeMC 7o76C 7oagC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12775.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Plectasin double strands | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : supermolecular assembly of plectasin into two protein fibrils
Entire | Name: supermolecular assembly of plectasin into two protein fibrils |
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Components |
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-Supramolecule #1: supermolecular assembly of plectasin into two protein fibrils
Supramolecule | Name: supermolecular assembly of plectasin into two protein fibrils type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pseudoplectania nigrella (fungus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Fungal defensin plectasin
Macromolecule | Name: Fungal defensin plectasin / type: protein_or_peptide / ID: 1 / Number of copies: 42 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudoplectania nigrella (fungus) |
Molecular weight | Theoretical: 4.402092 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GFGCNGPWSE DDMKCHNHCK SIKGYKGGYC AKGGFLCKCY |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |