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- EMDB-64861: Cryo-EM structure of the ArlB filament of Haloarcula marismortui -

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Basic information

Entry
Database: EMDB / ID: EMD-64861
TitleCryo-EM structure of the ArlB filament of Haloarcula marismortui
Map data
Sample
  • Complex: ArlB 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 / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / structural molecule activity / Flagellin
Function and homology information
Biological speciesHaloarcula marismortui (Halophile)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 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
DepositionMay 30, 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_64861.png

Downloads & links

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Map

FileDownload / File: emd_64861.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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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: 0.35
Minimum - Maximum-2.1324916 - 3.1209161
Average (Standard dev.)0.003411661 (±0.12074368)
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: #1

Fileemd_64861_additional_1.map
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Half map: #2

Fileemd_64861_half_map_1.map
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Half map: #1

Fileemd_64861_half_map_2.map
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Sample components

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Entire : ArlB filament

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

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Supramolecule #1: ArlB filament

SupramoleculeName: ArlB 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: 33 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula marismortui (Halophile)
Molecular weightTheoretical: 46.839656 KDa
SequenceString: MFERITNPED RGQVGIGTLI VFIAMVLVAA IAAGVLINTA GFLQSSAEQT GQESSDQVTN QIQVASKIGS VAGSGPTDTI IVEGETIQF AIDSGSTLTV SSTSAGDSNL ANLDGQDGEV AVEQGDEIRF TRESTSTISV TNTETGASTT VSEGTDTLSL A GDSDTNDD ...String:
MFERITNPED RGQVGIGTLI VFIAMVLVAA IAAGVLINTA GFLQSSAEQT GQESSDQVTN QIQVASKIGS VAGSGPTDTI IVEGETIQF AIDSGSTLTV SSTSAGDSNL ANLDGQDGEV AVEQGDEIRF TRESTSTISV TNTETGASTT VSEGTDTLSL A GDSDTNDD TVTFQRTYED PVNGEVDITS VTLNDGESTS AVSADLENSQ NTEQYLPLTG DDSNSDDVIV SDGETLSATS GS SDITVAS STITINQGDD VTFDVIANDE VRITNENTGD SVSFNPFDNQ IDTASALTLE NDDGDQIITT SSGQITGLAS SEV SLTTSQ VLLVNEDYST GGGGVSEISV IAIKGSGADQ INLEQTTITT IGPSGTNTLT YGGNSATEGE TFGVQAVQDE DDSL PVMTD ADRFRIIVNP GTLETGETMT LEVTTESGAT TEIRVSVPNT LSGETAVQV

UniProtKB: Flagellin

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 33
Molecular weightTheoretical: 22.99 Da

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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: 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: 30.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5z1l

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 372368
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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