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- EMDB-52629: Structure of the bacterial archaellum from L. aerophila -

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Basic information

Entry
Database: EMDB / ID: EMD-52629
TitleStructure of the bacterial archaellum from L. aerophila
Map data
Sample
  • Organelle or cellular component: Archaellum filament of L. aerophila
    • Protein or peptide: Flagellin
KeywordsHelical / cell surface structure / motility / archaellum / PROTEIN FIBRIL
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 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: Biorxiv / Year: 2025
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 SV
History
DepositionJan 28, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52629.png

Downloads & links

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Map

FileDownload / File: emd_52629.map.gz / Format: CCP4 / Size: 63.3 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 255 pix.
= 244.8 Å		0.96 Å/pix.
x 255 pix.
= 244.8 Å		0.96 Å/pix.
x 255 pix.
= 244.8 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: 0.023
Minimum - Maximum-0.025510956 - 0.059709243
Average (Standard dev.)0.0004965826 (±0.0038878853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions255255255
Spacing255255255
CellA=B=C: 244.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52629_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_52629_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 : Archaellum filament of L. aerophila

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

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Supramolecule #1: Archaellum filament of L. aerophila

SupramoleculeName: 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: 17 / Enantiomer: LEVO
Source (natural)Organism: Litorilinea aerophila (bacteria) / Strain: DSM:25763
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
Processinghelical 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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
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

Final reconstructionNumber classes used: 20
Applied symmetry - Helical parameters - Δz: 5.64 Å
Applied symmetry - Helical parameters - Δ&Phi: 108.14 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6) / Number images used: 1610077
CTF correctionType: NONE
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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