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- EMDB-19112: Cuniculiplasma divulgatum filament -

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Basic information

Entry
Database: EMDB / ID: EMD-19112
TitleCuniculiplasma divulgatum filament
Map data
Sample
  • Organelle or cellular component: Cuniculiplasma divulgatum type IV filament
    • Protein or peptide: Flagellin-like protein
Keywordscell surface appendage / N-glycosylation / PROTEIN FIBRIL
Function / homologyArchaeal Type IV pilin, N-terminal / Archaeal Type IV pilin, N-terminal / Flagellin/pilin, N-terminal / membrane / Flagellin-like protein
Function and homology information
Biological speciesCuniculiplasma divulgatum (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.61 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 12, 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_19112.png

Downloads & links

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Map

FileDownload / File: emd_19112.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.040326614 - 0.17806588
Average (Standard dev.)0.0013740506 (±0.009652885)
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_19112_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19112_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cuniculiplasma divulgatum type IV filament

EntireName: Cuniculiplasma divulgatum type IV filament
Components
  • Organelle or cellular component: Cuniculiplasma divulgatum type IV filament
    • Protein or peptide: Flagellin-like protein

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Supramolecule #1: Cuniculiplasma divulgatum type IV filament

SupramoleculeName: Cuniculiplasma divulgatum type IV filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cuniculiplasma divulgatum (archaea)

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Macromolecule #1: Flagellin-like protein

MacromoleculeName: Flagellin-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Cuniculiplasma divulgatum (archaea)
Molecular weightTheoretical: 13.504127 KDa
SequenceString:
VSPIIATILL IAITVVLAAT LVTILGGFTH GVSNTVETAG VTSHITSKYI FINVSSSSSA ISASSITITI TGASFKVTSG DTLAEVAGV SSTSSNATFT GGSDYTVPIS LSSSQTVAGV SFELIYKGNV IYNSAA

UniProtKB: Flagellin-like protein

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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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.4 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: 5.188 Å
Applied symmetry - Helical parameters - Δ&Phi: 106.047 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 645487
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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