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- EMDB-54927: Structure of the bacterial archaellum from L. aerophila -

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Basic information

Entry
Database: EMDB / ID: EMD-54927
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: Nat Microbiol / Year: 2025
Title: Structure of a functional archaellum in Bacteria of the Chloroflexota phylum.
Authors: Shamphavi Sivabalasarma / Najwa Taib / Clara L Mollat / Marie Joest / Stefan Steimle / Simonetta Gribaldo / Sonja-Verena Albers /
Abstract: Motility in Archaea is driven by the archaellum, a rotary ATP-driven machinery unrelated to the bacterial flagellum. To date, archaella have been described exclusively in archaea; however, recent ...Motility in Archaea is driven by the archaellum, a rotary ATP-driven machinery unrelated to the bacterial flagellum. To date, archaella have been described exclusively in archaea; however, recent work reported archaellum genes in bacterial strains of the SAR202 clade (Chloroflexota). Here, using MacSyFinder, we show that bona fide archaellum gene clusters are widespread in several members of the Chloroflexota. Analysis of archaellum-encoding loci and Alphafold3-predicted structures show similarity to the archaellum machinery. Using cryo electron microscopy single-particle analysis, we solved the structure of the bacterial archaellum from Litorilinea aerophila to 2.7 Å. We also show the expression and assembly of this machinery in bacteria and its function in swimming motility. Finally, a phylogenomic analysis revealed two horizontal gene transfer events from euryarchaeal members to Chloroflexota. In summary, our study shows that a functional and assembled archaellum machinery can be exchanged between the two prokaryotic domains.
History
DepositionAug 28, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54927.png

Downloads & links

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Map

FileDownload / File: emd_54927.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.48 Å/pix.
x 512 pix.
= 245.76 Å		0.48 Å/pix.
x 512 pix.
= 245.76 Å		0.48 Å/pix.
x 512 pix.
= 245.76 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.04756661 - 0.10387196
Average (Standard dev.)0.00092437014 (±0.007090802)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54927_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54927_half_map_2.map
Projections & Slices
AxesZYX

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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)
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
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 reconstructionApplied 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: 1302899
CTF correctionType: NONE
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9sie:
Structure of the bacterial archaellum from L. aerophila

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