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- EMDB-67194: Cryo-EM structure of ArlA2 filament of Haloarcula marismortui -

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Basic information

Entry
Database: EMDB / ID: EMD-67194
TitleCryo-EM structure of ArlA2 filament of Haloarcula marismortui
Map data
Sample
  • Complex: ArlA2 filament
    • Protein or peptide: Flagellin
  • Ligand: SODIUM ION
Keywordsarchaellum / haloarcheon / PROTEIN FIBRIL
Function / homologyarchaeal-type flagellum / Flagellin, archaea / Archaeal-type flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / Flagellin
Function and homology information
Biological speciesHaloarcula marismortui (Halophile)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMeshcheryakov VA / Hyun J / Syutkin AS / Pyatibratov MG / Wolf M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Other government Japan
CitationJournal: Nat Commun / Year: 2026
Title: Two types of sheathed archaellum structures from Haloarcula marismortui differ in their outer layer architectures.
Authors: Vladimir A Meshcheryakov / Jaekyung Hyun / Satoshi Shibata / Alexey S Syutkin / Mikhail G Pyatibratov / Matthias Wolf /
Abstract: Many archaea swim by means of rotating helical filaments called archaella. Most archaella are about 10 nm in diameter and comprise multiple copies of the protein archaellin. Here, we describe two ...Many archaea swim by means of rotating helical filaments called archaella. Most archaella are about 10 nm in diameter and comprise multiple copies of the protein archaellin. Here, we describe two archaellum structures formed by the ArlA2 or ArlB archaellins from the haloarchaeon Haloarcula marismortui. We found that both filaments have an additional proteinaceous outer sheath surrounding their inner core, a feature not observed previously in archaea. The outer sheath structures of the two filaments differ fundamentally. The outer domain of ArlB archaellin rotates by 180, forming stable dimers that likely increase the filament rigidity. In contrast, neither rotation nor dimerization of the outer domain was observed in ArlA2 filaments. 3D variability analysis demonstrated that the motions of ArlA2 and ArlB filaments are significantly distinct. Additionally, the ArlB filament displays a larger negatively charged surface area than ArlA2, which may help adaptation to higher salt concentrations. Our structural findings provide insight into how the two filaments can adapt to their different environments. Larger archaellins with additional outer domains can be found in various groups of archaea. We propose that such proteins may allow hosts to modify the properties of their archaella to enhance environmental adaptation.
History
DepositionNov 22, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67194.png

Downloads & links

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Map

FileDownload / File: emd_67194.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 433.2 Å		1.08 Å/pix.
x 400 pix.
= 433.2 Å		1.08 Å/pix.
x 400 pix.
= 433.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.2625886 - 2.1605053
Average (Standard dev.)0.003985627 (±0.07508204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 433.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Focused refined map

Fileemd_67194_additional_1.map
AnnotationFocused refined map
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AxesZYX

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Half map: #1

Fileemd_67194_half_map_1.map
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Half map: #2

Fileemd_67194_half_map_2.map
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Sample components

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Entire : ArlA2 filament

EntireName: ArlA2 filament
Components
  • Complex: ArlA2 filament
    • Protein or peptide: Flagellin
  • Ligand: SODIUM ION

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Supramolecule #1: ArlA2 filament

SupramoleculeName: ArlA2 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Haloarcula marismortui (Halophile)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula marismortui (Halophile)
Molecular weightTheoretical: 47.382547 KDa
SequenceString: MFEKIANENE RGQVGIGTLI VFIAMVLVAA IAAGVLINTA GFLQSSAEQT GQESSDQVTN QIQVASKVGI VGGQGASDTI AIQSPSGNQ FAIESGSTVT ATEVTDNNDD GYILVDSPQG NELAVDGGDQ IRLTRESGSQ VEITNEDTGV SITSSKLDLK D ASGSDTLK ...String:
MFEKIANENE RGQVGIGTLI VFIAMVLVAA IAAGVLINTA GFLQSSAEQT GQESSDQVTN QIQVASKVGI VGGQGASDTI AIQSPSGNQ FAIESGSTVT ATEVTDNNDD GYILVDSPQG NELAVDGGDQ IRLTRESGSQ VEITNEDTGV SITSSKLDLK D ASGSDTLK FVRTYEDPVN GQLQLQSVTI DNTGTADSTD DGVSATLSTG ENTEKYIPLT DGSSKAIIGN GETVTVTSDS DS GSTLSAG AETLSVDPGD EVLFEVTGDS EVTITNQESG SSISYNPLDG SNYLSGTAGS GSTLKLSVSD DGSATSLDVT SGL TGLTTG DFATGPGNEI QLVNEDYNAG GGGVGTLNIV AIKGSGADQI NMEETTITTI GPDGTNTLTY SDDGATEDQT FAVE SIQDD DDSLPVMTDS DRFRVVIDPG TLETGETMTL EVTTESGATT EIRISVPNTL AGESAVQV

UniProtKB: Flagellin

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 28
Molecular weightTheoretical: 22.99 Da

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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: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.53 Å
Applied symmetry - Helical parameters - Δ&Phi: 108.19 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 309194
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5z1l

Final angle assignmentType: MAXIMUM LIKELIHOOD

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