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- EMDB-53582: Supercoiling bacterial archaellum filament from L. aerophila -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-53582
TitleSupercoiling bacterial archaellum filament from L. aerophila
Map data
Sample
  • Organelle or cellular component: supercoiling archaellum filament of L. aerophila
    • Protein or peptide: Flagellin
KeywordsHelical / cell surface structure / motility / archaellum / PROTEIN FIBRIL / Supercoiling / Superhelicity
Function / homologyFlagellin, archaea / Archaeal-type flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / membrane / Flagellin
Function and homology information
Biological speciesLitorilinea aerophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSivabalasarma S / Taib N / Mollat CL / Joest M / Steimle S / Gribaldo S / Albers S-V
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)403222702 Germany
CitationJournal: To Be Published
Title: Horizontal gene transfer of the functional archaellum machinery to Bacteria
Authors: Sivabalasarma S / Taib N / Mollat CL / Joest M / Steimle S / Gribaldo S / Albers S-V
History
DepositionMay 8, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53582.png

Downloads & links

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Map

FileDownload / File: emd_53582.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.3141274 - 1.8917117
Average (Standard dev.)0.0017012522 (±0.045190107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 491.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53582_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53582_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : supercoiling archaellum filament of L. aerophila

EntireName: supercoiling archaellum filament of L. aerophila
Components
  • Organelle or cellular component: supercoiling archaellum filament of L. aerophila
    • Protein or peptide: Flagellin

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Supramolecule #1: supercoiling archaellum filament of L. aerophila

SupramoleculeName: supercoiling archaellum filament of L. aerophila / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Archaellum filament isolated from the cell surface of L. aerophila
Source (natural)Organism: Litorilinea aerophila (bacteria) / Strain: DSM:25763 / Location in cell: cell surface

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 42 / Enantiomer: LEVO
Source (natural)Organism: Litorilinea aerophila (bacteria) / Strain: DSM25763
Molecular weightTheoretical: 19.468656 KDa
SequenceString:
ITALETAIIL IAFVVVASVF AFTILSAGTF STERGKEAVY AGLSEVRSSI EIKGSVVIIG ETTGATGTVD SVIFTVASAA GGEPIDLNN DPDDRVVVID YRDATQRHTD VDWSVTWLGK NDYDTTGDTL LEQGELAEIT VTLAPTITLS TNTDFIIEVK P PAGAVFSI QRTTPAYIET VNDLQ

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
2.0 %NaClsodium chloride
1.0 xPBSphosphate buffered saline

Details: 2% NaCl in 1x PBS, pH 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Detailssheared and purified archaella filament from L. aerophila

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1805195
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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