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- PDB-9v96: Cryo-EM structure of the inner core of ArlA2 filament of Haloarcu... -

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Basic information

Entry
Database: PDB / ID: 9v96
TitleCryo-EM structure of the inner core of ArlA2 filament of Haloarcula marismortui
ComponentsFlagellin
KeywordsPROTEIN FIBRIL / archaellum / haloarcheon
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsMeshcheryakov, V.A. / Hyun, J. / Syutkin, A.S. / Pyatibratov, M.G. / Wolf, M.
Funding support Japan, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin
W: Flagellin
X: Flagellin
Y: Flagellin
Z: Flagellin
a: Flagellin
b: Flagellin
d: Flagellin
e: Flagellin
f: Flagellin
g: Flagellin
i: Flagellin
j: Flagellin
k: Flagellin
l: Flagellin
m: Flagellin
n: Flagellin
o: Flagellin
p: Flagellin
B: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,801,41076
Polymers1,800,53738
Non-polymers87438
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellin


Mass: 47382.547 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: Q5V881
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ArlA2 filament / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Haloarcula marismortui (Halophile)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21_5207model refinement
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 309194 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 84.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002348289
ELECTRON MICROSCOPYf_angle_d0.510265842
ELECTRON MICROSCOPYf_chiral_restr0.04298587
ELECTRON MICROSCOPYf_plane_restr0.00328662
ELECTRON MICROSCOPYf_dihedral_angle_d3.65176769

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