[English] 日本語
Yorodumi
- EMDB-52650: Recombinant F-ENA-2 fibers -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52650
TitleRecombinant F-ENA-2 fibers
Map data
Sample
  • Complex: Recombinant F-ENA-2 fibers
    • Protein or peptide: DUF4183 domain-containing protein
Keywordsendospore appendage / ENA / helical / protein fiber / bacillus thuringiensis serovar kurstaki / PROTEIN FIBRIL
Function / homologyDomain of unknown function DUF4183 / Domain of unknown function (DUF4183) / membrane / DUF4183 domain-containing protein
Function and homology information
Biological speciesCohnella sp. OV330 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsSleutel M / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G043021N Belgium
CitationJournal: bioRxiv / Year: 2025
Title: Cryo-EM analysis of the extrasporal matrix identifies F-ENA as a widespread family of endospore appendages across the Firmicutes phylum.
Authors: Mike Sleutel / Adrià Sogues / Nani Van Gerven / Unni Lise Jonsmoen / Inge Van Molle / Marcus Fislage / Laurent Dirk Theunissen / Nathan F Bellis / Diana P Baquero / Edward H Egelman / Mart ...Authors: Mike Sleutel / Adrià Sogues / Nani Van Gerven / Unni Lise Jonsmoen / Inge Van Molle / Marcus Fislage / Laurent Dirk Theunissen / Nathan F Bellis / Diana P Baquero / Edward H Egelman / Mart Krupovic / Fengbin Wang / Marina Aspholm / Han Remaut /
Abstract: For over 100 years, (Bt) has been used as an agricultural biopesticide to control pests caused by insect species in the orders of Lepidoptera, Diptera and Coleoptera. Under nutrient starvation, Bt ...For over 100 years, (Bt) has been used as an agricultural biopesticide to control pests caused by insect species in the orders of Lepidoptera, Diptera and Coleoptera. Under nutrient starvation, Bt cells differentiate into spores and associated toxin crystals that can adopt biofilm-like aggregates. We reveal that such Bt spore/toxin biofilms are embedded in a fibrous extrasporal matrix (ESM), and using cryoID, we resolved the structure and molecular identity of an uncharacterized type of pili, referred to here as Fibrillar ENdospore Appendages or 'F-ENA'. F-ENA are monomolecular protein polymers tethered to the exosporium of Bt and are decorated with a flexible tip fibrillum. Phylogenetic analysis reveals that F-ENA is widespread not only in the class Bacilli, but also in the class Clostridia, and the cryoEM structures of F-ENA filaments from and reveal subunits with a generic head-neck domain structure, where the β-barrel neck of variable length latch onto a preceding head domain through short N-terminal hook peptides. In , two collagen-like proteins (CLP) respectively tether F-ENA to the exosporium (F-Anchor), or constitute the tip fibrillum at the distal terminus of F-ENA (F-BclA). Sedimentation assays point towards F-ENA involvement in spore-spore clustering, likely mediated via F-BclA contacts and F-ENA bundling through the antiparallel interlocking of the head-neck units.
History
DepositionJan 29, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52650.png

Downloads & links

-
Map

FileDownload / File: emd_52650.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 300 pix.
= 426. Å		1.42 Å/pix.
x 300 pix.
= 426. Å		1.42 Å/pix.
x 300 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-1.188073 - 1.7222248
Average (Standard dev.)0.00059856253 (±0.017734608)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 426.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52650_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: EMREADY post-processed

Fileemd_52650_additional_1.map
AnnotationEMREADY post-processed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52650_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52650_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Recombinant F-ENA-2 fibers

EntireName: Recombinant F-ENA-2 fibers
Components
  • Complex: Recombinant F-ENA-2 fibers
    • Protein or peptide: DUF4183 domain-containing protein

-
Supramolecule #1: Recombinant F-ENA-2 fibers

SupramoleculeName: Recombinant F-ENA-2 fibers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cohnella sp. OV330 (bacteria)

-
Macromolecule #1: DUF4183 domain-containing protein

MacromoleculeName: DUF4183 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Cohnella sp. OV330 (bacteria)
Molecular weightTheoretical: 13.423285 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPVIKPVIVA VSSAPVSTGG VIATTVSPTV ARFYAAITAA MIAGGVTTIP AASFLDDADA PVAALPVPAA NGYYNVYING ILQQGGLST LTAVSLALAS GDFVEGTPVL LEVGTFGGDS TLTTQPTISA PTITIIS

UniProtKB: DUF4183 domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 95.25 Å
Applied symmetry - Helical parameters - Δ&Phi: 67.50 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 286873
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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://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