[English] 日本語
Yorodumi
- PDB-7oag: Cryo-EM structure of the plectasin fibril (single strand) -

+
Open data


ID or keywords:

Loading...

-
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 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more