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- EMDB-19168: Oxiplasma meridianum archaellum -

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Basic information

Entry
Database: EMDB / ID: EMD-19168
TitleOxiplasma meridianum archaellum
Map data
Sample
  • Organelle or cellular component: Oxiplasma meridianum archaellum
    • Protein or peptide: Oxiplasma meridianum archaellum
  • Ligand: beta-D-galactopyranose
Keywordscell surface appendage / N-glycosylation / PROTEIN FIBRIL
Biological speciesOxyplasma meridianum (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsIsupov MN / Gaines M / Daum B / McLaren M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: ISME J / Year: 2025
Title: Unusual cell surfaces, pili, and archaella of Thermoplasmatales archaea.
Authors: Matthew C Gaines / Michail N Isupov / Mathew McLaren / Risat Ul Haque / Alejandra Recalde / Rafael Bargiela / Vicki A M Gold / Sonja-Verena Albers / Peter N Golyshin / Olga V Golyshina / Bertram Daum /
Abstract: Archaea of the order Thermoplasmatales push the boundaries of our current knowledge of prokaryotic life. They show distinct cellular plasticity, heterogenous cell morphologies, and lack a ...Archaea of the order Thermoplasmatales push the boundaries of our current knowledge of prokaryotic life. They show distinct cellular plasticity, heterogenous cell morphologies, and lack a paracrystalline S-layer. As the S-layer has previously been implicated in acting as a stator scaffold for filaments driving cellular propulsion, particularly archaella, we asked whether the absence of an S-layer precludes the formation of functional archaella or pili in Thermoplasmatales. Using cryoEM, we investigated the two Thermoplasmatales species Cuniculiplasma divulgatum and Oxyplasma meridianum. We found that these species indeed generate pili and archaella and that the latter likely function in cellular propulsion. Whereas C. divulgatum produces pili with terminal hooks using a unique assembly machinery, O. meridianum generates unusually wide, "barbed" archaella with a high degree of glycosylation. Our results show that for the generation of functional archaella and pili, a canonical S-layer is not necessary.
History
DepositionDec 14, 2023-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19168.png

Downloads & links

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Map

FileDownload / File: emd_19168.map.gz / Format: CCP4 / Size: 103 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.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.043801133 - 0.16378058
Average (Standard dev.)0.0013867731 (±0.010521071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19168_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_19168_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Oxiplasma meridianum archaellum

EntireName: Oxiplasma meridianum archaellum
Components
  • Organelle or cellular component: Oxiplasma meridianum archaellum
    • Protein or peptide: Oxiplasma meridianum archaellum
  • Ligand: beta-D-galactopyranose

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Supramolecule #1: Oxiplasma meridianum archaellum

SupramoleculeName: Oxiplasma meridianum archaellum / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oxyplasma meridianum (archaea)

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Macromolecule #1: Oxiplasma meridianum archaellum

MacromoleculeName: Oxiplasma meridianum archaellum / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO
Source (natural)Organism: Oxyplasma meridianum (archaea)
Molecular weightTheoretical: 23.887668 KDa
SequenceString: ETGIGTLIIF IAMVLVAAVA ATVLINTAGS LQQRATSTGS QTTNQVSTGL IVQSIYGMDN NRSNPESGSL NWTAIYVTLN TGSSPVDLS NVSLSLEYQG QLASLKYTPA TTNASFAVDT NGTSNVFSVL NAGVGYKNST ATFKNVELKN VTKSTNFAIV V IRDPSNSL ...String:
ETGIGTLIIF IAMVLVAAVA ATVLINTAGS LQQRATSTGS QTTNQVSTGL IVQSIYGMDN NRSNPESGSL NWTAIYVTLN TGSSPVDLS NVSLSLEYQG QLASLKYTPA TTNASFAVDT NGTSNVFSVL NAGVGYKNST ATFKNVELKN VTKSTNFAIV V IRDPSNSL TSSHPVLTTG SEVVILVNTS AVFGGMKQGQ AVTGQINPSV GSPGIIQFTT PSAFTETVME LQ

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Macromolecule #5: beta-D-galactopyranose

MacromoleculeName: beta-D-galactopyranose / type: ligand / ID: 5 / Number of copies: 64 / Formula: GAL
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GAL:
beta-D-galactopyranose

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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: 1
VitrificationCryogen name: ETHANE
DetailsOxiplasma meridianum archaellum

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.45 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.641 Å
Applied symmetry - Helical parameters - Δ&Phi: 107.922 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1374113
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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