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- EMDB-19960: Sulfolobus acidocaldarius AAP filament -

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Basic information

Entry
Database: EMDB / ID: EMD-19960
TitleSulfolobus acidocaldarius AAP filament
Map data
Sample
  • Organelle or cellular component: Filament
    • Protein or peptide: DUF4352 domain-containing protein
Keywordscell surface appendage / N-glycosylation / PROTEIN FIBRIL
Function / homologyImmunoglobulin-like fold / membrane / DUF4352 domain-containing protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 2.6 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 26, 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_19960.png

Downloads & links

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Map

FileDownload / File: emd_19960.map.gz / Format: CCP4 / Size: 91.1 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.)
1.07 Å/pix.
x 288 pix.
= 308.736 Å		1.07 Å/pix.
x 288 pix.
= 308.736 Å		1.07 Å/pix.
x 288 pix.
= 308.736 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.041
Minimum - Maximum-0.04700868 - 0.16912073
Average (Standard dev.)0.0009849793 (±0.009853341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 308.73602 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19960_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: #2

Fileemd_19960_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Filament

EntireName: Filament
Components
  • Organelle or cellular component: Filament
    • Protein or peptide: DUF4352 domain-containing protein

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Supramolecule #1: Filament

SupramoleculeName: Filament / 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: 37 / 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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 22790 / Average exposure time: 2.57 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: 2.1 µm / Nominal defocus min: 0.5 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: 15.52 Å
Applied symmetry - Helical parameters - Δ&Phi: -39.86 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 505862
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsJligand was used for preparing dictionaries for an unusual sugars
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ets:
Sulfolobus acidocaldarius AAP filament

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