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- EMDB-13546: Sulfolobus acidocaldarius 0406 filament. -

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Basic information

Entry
Database: EMDB / ID: EMD-13546
TitleSulfolobus acidocaldarius 0406 filament.
Map data
Sample
  • Organelle or cellular component: Filament
    • Protein or peptide: Sulfolobus acidocaldarius 0406 filament.
Keywordscell surface appendage / beta-strand addition / isopeptide bond / N-glycosylation / beta-sandwich / PROTEIN FIBRIL
Function / homologyUncharacterized protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsIsupov MN / Gaines M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: Nat Commun / Year: 2022
Title: Electron cryo-microscopy reveals the structure of the archaeal thread filament.
Authors: Matthew C Gaines / Michail N Isupov / Shamphavi Sivabalasarma / Risat Ul Haque / Mathew McLaren / Clara L Mollat / Patrick Tripp / Alexander Neuhaus / Vicki A M Gold / Sonja-Verena Albers / Bertram Daum /
Abstract: Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal ...Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.
History
DepositionSep 6, 2021-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13546.png

Downloads & links

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Map

FileDownload / File: emd_13546.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 402.048 Å		1.05 Å/pix.
x 384 pix.
= 402.048 Å		1.05 Å/pix.
x 384 pix.
= 402.048 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1638
Minimum - Maximum-0.015122809 - 1.5670989
Average (Standard dev.)0.00060520147 (±0.015186864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 402.04803 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Filament

EntireName: Filament
Components
  • Organelle or cellular component: Filament
    • Protein or peptide: Sulfolobus acidocaldarius 0406 filament.

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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: Sulfolobus acidocaldarius 0406 filament.

MacromoleculeName: Sulfolobus acidocaldarius 0406 filament. / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)
Molecular weightTheoretical: 22.291539 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius (acidophilic)
SequenceString: MNKKRLLLLS VFLVSVFVPV LVADVIYYYQ GQITVGNVAP PMYFAIQPNG NAKIGNNSNV PSYINAQPSS GGSGFTAQVN ITNATYNYY FNFMGLAVSK TGYIYLAKVA YSYTATNNPI QNATLYIMNQ QGQIVYKYKL IVNGVVNSTL PSTPLQINSG S YIVSLLIV ...String:
MNKKRLLLLS VFLVSVFVPV LVADVIYYYQ GQITVGNVAP PMYFAIQPNG NAKIGNNSNV PSYINAQPSS GGSGFTAQVN ITNATYNYY FNFMGLAVSK TGYIYLAKVA YSYTATNNPI QNATLYIMNQ QGQIVYKYKL IVNGVVNSTL PSTPLQINSG S YIVSLLIV PYQGTLPKTP SNDLATITVN FGFSPMTASP PPIPLPSP

UniProtKB: Uncharacterized 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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 6272 / Average electron dose: 42.33 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 31.649 Å
Applied symmetry - Helical parameters - Δ&Phi: -103.234 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 188620
Segment selectionNumber selected: 410270 / Software - Name: cryoSPARC (ver. 3.2.0)
Software - details: cryoSPARC filament tracer was used to automatically pick particles
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.2.0)

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Atomic model buiding 1

DetailsJligand was used for preparing dictionaries for an unusual sugars and an isopeptide link beween main chain nitrogen of the N-terminal D25 and C gamma of N57 from N-2 monomer in the filament.
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-7pnb:
Sulfolobus acidocaldarius 0406 filament.

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