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- EMDB-19990: Structure of the AAP filament of Sulfolobus acidocaldarius strain... -

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Entry
Database: EMDB / ID: EMD-19990
TitleStructure of the AAP filament of Sulfolobus acidocaldarius strain MW039 (delta agl3 mutant).
Map data
Sample
  • Organelle or cellular component: Aap filament of the S. acidocaldarius species deficient in sulfoquinovose transferase enzyme
    • Protein or peptide: DUF4352 domain-containing protein
Keywordscell surface appendage / N-glycosylation / mutagenesis / PROTEIN FIBRIL
Function / homologyImmunoglobulin-like fold / membrane / DUF4352 domain-containing protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsDaum B / Isupov MN / Gaines M / McLaren M / Mollat C
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: Nat Commun / Year: 2024
Title: Towards a molecular picture of the archaeal cell surface.
Authors: Matthew C Gaines / Michail N Isupov / Mathew McLaren / Clara L Mollat / Risat Ul Haque / Jake K Stephenson / Shamphavi Sivabalasarma / Cyril Hanus / Daniel Kattnig / Vicki A M Gold / Sonja ...Authors: Matthew C Gaines / Michail N Isupov / Mathew McLaren / Clara L Mollat / Risat Ul Haque / Jake K Stephenson / Shamphavi Sivabalasarma / Cyril Hanus / Daniel Kattnig / Vicki A M Gold / Sonja Albers / Bertram Daum /
Abstract: Archaea produce various protein filaments with specialised functions. While some archaea produce only one type of filament, the archaeal model species Sulfolobus acidocaldarius generates four. These ...Archaea produce various protein filaments with specialised functions. While some archaea produce only one type of filament, the archaeal model species Sulfolobus acidocaldarius generates four. These include rotary swimming propellers analogous to bacterial flagella (archaella), pili for twitching motility (Aap), adhesive fibres (threads), and filaments facilitating homologous recombination upon UV stress (UV pili). Here, we use cryo-electron microscopy to describe the structure of the S. acidocaldarius archaellum at 2.0 Å resolution, and update the structures of the thread and the Aap pilus at 2.7 Å and 2.6 Å resolution, respectively. We define features unique to archaella of the order Sulfolobales and compare their structure to those of Aap and threads in the context of the S-layer. We define distinct N-glycan patterns in the three filaments and identify a putative O-glycosylation site in the thread. Finally, we ascertain whether N-glycan truncation leads to structural changes in archaella and Aap.
History
DepositionMar 28, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19990.png

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Map

FileDownload / File: emd_19990.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 288 pix.
= 265.248 Å		0.92 Å/pix.
x 288 pix.
= 265.248 Å		0.92 Å/pix.
x 288 pix.
= 265.248 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.051365126 - 0.15507545
Average (Standard dev.)0.00067538576 (±0.008387598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 265.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19990_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_19990_half_map_2.map
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Sample components

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Entire : Aap filament of the S. acidocaldarius species deficient in sulfoq...

EntireName: Aap filament of the S. acidocaldarius species deficient in sulfoquinovose transferase enzyme
Components
  • Organelle or cellular component: Aap filament of the S. acidocaldarius species deficient in sulfoquinovose transferase enzyme
    • Protein or peptide: DUF4352 domain-containing protein

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Supramolecule #1: Aap filament of the S. acidocaldarius species deficient in sulfoq...

SupramoleculeName: Aap filament of the S. acidocaldarius species deficient in sulfoquinovose transferase enzyme
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)

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Macromolecule #1: DUF4352 domain-containing protein

MacromoleculeName: DUF4352 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)
Molecular weightTheoretical: 14.177022 KDa
SequenceString:
LSGAIVALIL VIAGVIIAIA VVLFAFGLIP GISNQGSIQV LGSGTITNST ASGSSRTIYN ITITVKNTGT TSISVTSINI NGQPFNING TAPSIPAGRT QPITFEVTPA SGKPNFSPGA SYTATIYFSN GQGAPATLIY QG

UniProtKB: DUF4352 domain-containing 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: 3
VitrificationCryogen name: ETHANE
DetailsMixed population of filaments isolated from Sulfolobus acidocaldarius deficient in agl3 - UDP-sulfoquinovose synthase

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: EPU (ver. 3.5)
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 29189 / Average exposure time: 4.5 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 15.282 Å
Applied symmetry - Helical parameters - Δ&Phi: -39.953 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 691479
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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