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- EMDB-52871: Ex vivo spore-silk A-ENA fibers -

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Basic information

Entry
Database: EMDB / ID: EMD-52871
TitleEx vivo spore-silk A-ENA fibers
Map data
Sample
  • Cell: Ex vivo spore-silk A-ENA fibers
    • Protein or peptide: Ex vivo spore-silk A-ENA fibers
  • Ligand: water
Keywordsendospore / isopeptide bond / A-ENA / cross-linked / protein fiber / autocatalytic / PROTEIN FIBRIL
Function / homology: / Alpha-helical endospore appendage domain / Uncharacterized protein
Function and homology information
Biological speciesBacillus thuringiensis serovar israelensis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSleutel M / Sogues A / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionFeb 21, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52871.png

Downloads & links

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Map

FileDownload / File: emd_52871.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 300 pix.
= 229.8 Å		0.77 Å/pix.
x 300 pix.
= 229.8 Å		0.77 Å/pix.
x 300 pix.
= 229.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.766 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0606
Minimum - Maximum-0.011374843 - 0.13657366
Average (Standard dev.)0.0023664031 (±0.009777184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 229.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52871_msk_1.map
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Additional map: #1

Fileemd_52871_additional_1.map
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Half map: #1

Fileemd_52871_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_52871_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ex vivo spore-silk A-ENA fibers

EntireName: Ex vivo spore-silk A-ENA fibers
Components
  • Cell: Ex vivo spore-silk A-ENA fibers
    • Protein or peptide: Ex vivo spore-silk A-ENA fibers
  • Ligand: water

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Supramolecule #1: Ex vivo spore-silk A-ENA fibers

SupramoleculeName: Ex vivo spore-silk A-ENA fibers / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus thuringiensis serovar israelensis (bacteria)

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Macromolecule #1: Ex vivo spore-silk A-ENA fibers

MacromoleculeName: Ex vivo spore-silk A-ENA fibers / type: protein_or_peptide / ID: 1 / Number of copies: 29 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis serovar israelensis (bacteria)
Molecular weightTheoretical: 10.91755 KDa
Recombinant expressionOrganism: Bacillus thuringiensis serovar israelensis (bacteria)
SequenceString:
MGMPTIPEGL DITRDQAINI ILASIGLEEL GLAHVINAEG EKVQAVVAGF EKETVTFDQL LATNESVTQT LKTVIKKEML LQFKLEEAK SLIQSSSPPS IS

UniProtKB: Uncharacterized protein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 599 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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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: 3000 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.37 Å
Applied symmetry - Helical parameters - Δ&Phi: -173.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 532909
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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