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- PDB-9r50: Supercoiling bacterial archaellum filament from L. aerophila -

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Basic information

Entry
Database: PDB / ID: 9r50
TitleSupercoiling bacterial archaellum filament from L. aerophila
ComponentsFlagellin
KeywordsPROTEIN FIBRIL / Helical / cell surface structure / motility / archaellum / Supercoiling / Superhelicity
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSivabalasarma, S. / Taib, N. / Mollat, C.L. / Joest, M. / Steimle, S. / Gribaldo, S. / Albers, S.-V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)403222702 Germany
CitationJournal: To Be Published
Title: Horizontal gene transfer of the functional archaellum machinery to Bacteria
Authors: Sivabalasarma, S. / Taib, N. / Mollat, C.L. / Joest, M. / Steimle, S. / Gribaldo, S. / Albers, S.-V.
History
DepositionMay 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data 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
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin
W: Flagellin
X: Flagellin
Y: Flagellin
Z: Flagellin
An: Flagellin
Ao: Flagellin
Ap: Flagellin
Aq: Flagellin
Ar: Flagellin
At: Flagellin
Au: Flagellin
Aw: Flagellin
Ax: Flagellin
Ay: Flagellin
Az: Flagellin
A0: Flagellin
A1: Flagellin
A2: Flagellin
A3: Flagellin
A4: Flagellin
A5: Flagellin
A7: Flagellin
A8: Flagellin
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
J: Flagellin
N: Flagellin


Theoretical massNumber of molelcules
Total (without water)817,68442
Polymers817,68442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Flagellin


Mass: 19468.656 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Source: (natural) Litorilinea aerophila (bacteria) / Strain: DSM25763 / References: UniProt: A0A540VDN8
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: supercoiling archaellum filament of L. aerophila / Type: ORGANELLE OR CELLULAR COMPONENT
Details: Archaellum filament isolated from the cell surface of L. aerophila
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Litorilinea aerophila (bacteria) / Strain: DSM:25763 / Cellular location: cell surface
Buffer solutionpH: 7.4 / Details: 2% NaCl in 1x PBS, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
12 %sodium chlorideNaCl1
21 xphosphate buffered salinePBS1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: sheared and purified archaella filament from L. aerophila
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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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 / Calibrated magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1805195 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.68 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003558506
ELECTRON MICROSCOPYf_angle_d0.608480220
ELECTRON MICROSCOPYf_chiral_restr0.048310290
ELECTRON MICROSCOPYf_plane_restr0.00410206
ELECTRON MICROSCOPYf_dihedral_angle_d7.25658591

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