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- EMDB-41283: Cryo-EM of tri-pilus from S. islandicus REY15A -

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Basic information

Entry
Database: EMDB / ID: EMD-41283
TitleCryo-EM of tri-pilus from S. islandicus REY15A
Map dataCryo-EM map of tri-pilus
Sample
  • Complex: tri-pilus
    • Protein or peptide: DUF973 family protein
Keywordshelical symmetry / type iv pili / archaeal pilus / filament / PROTEIN FIBRIL
Function / homologymembrane / DUF973 family protein
Function and homology information
Biological speciesSulfolobus islandicus REY15A (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsEastep GN / Liu J / Rich-New ST / Egelman EH / Krupovic M / Wang F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Nat Commun / Year: 2024
Title: Two distinct archaeal type IV pili structures formed by proteins with identical sequence.
Authors: Junfeng Liu / Gunnar N Eastep / Virginija Cvirkaite-Krupovic / Shane T Rich-New / Mark A B Kreutzberger / Edward H Egelman / Mart Krupovic / Fengbin Wang /
Abstract: Type IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from small pilin proteins, can be many microns long and serve diverse ...Type IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from small pilin proteins, can be many microns long and serve diverse functions, including adhesion, biofilm formation, motility, and intercellular communication. Here, we determine atomic structures of two distinct adhesive T4P from Saccharolobus islandicus via cryo-electron microscopy (cryo-EM). Unexpectedly, both pili were assembled from the same pilin polypeptide but under different growth conditions. One filament, denoted mono-pilus, conforms to canonical archaeal T4P structures where all subunits are equivalent, whereas in the other filament, the tri-pilus, the same polypeptide exists in three different conformations. The three conformations in the tri-pilus are very different from the single conformation found in the mono-pilus, and involve different orientations of the outer immunoglobulin-like domains, mediated by a very flexible linker. Remarkably, the outer domains rotate nearly 180° between the mono- and tri-pilus conformations. Both forms of pili require the same ATPase and TadC-like membrane pore for assembly, indicating that the same secretion system can produce structurally very different filaments. Our results show that the structures of archaeal T4P appear to be less constrained and rigid than those of the homologous archaeal flagellar filaments that serve as helical propellers.
History
DepositionJul 19, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41283.png

Downloads & links

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Map

FileDownload / File: emd_41283.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of tri-pilus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.45676854 - 0.8577836
Average (Standard dev.)0.0047622686 (±0.031404324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_41283_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_41283_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tri-pilus

EntireName: tri-pilus
Components
  • Complex: tri-pilus
    • Protein or peptide: DUF973 family protein

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Supramolecule #1: tri-pilus

SupramoleculeName: tri-pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sulfolobus islandicus REY15A (archaea)

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Macromolecule #1: DUF973 family protein

MacromoleculeName: DUF973 family protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (archaea)
Molecular weightTheoretical: 14.053037 KDa
SequenceString:
MNMISRRKNA KALSGAVTAL ILVIASVIIA LVVVGFAFGL FGAFTGQGTV TQVGTATLSA GTGTLTVTLK NTGAATQVTG AIINGNAAS VSGQVTISAG QNTYSISLGG ISSSTLQNLV GSTISLTLQL SNGQTVTVSA IITS

UniProtKB: DUF973 family 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: 4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 15.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -39.65 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 240930
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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