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- EMDB-0397: Cryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-0397
TitleCryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus
Map dataprimary map
Sample
  • Complex: Sulfolobus islandicus LAL14/1 Pilus
    • Protein or peptide: M9UD72
Keywordshelical symmetry / archaeal pilus / STRUCTURAL PROTEIN
Function / homologymembrane / DUF973 family protein
Function and homology information
Biological speciesSulfolobus islandicus LAL14/1 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang F / Cvirkaite-Krupovic V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Nat Microbiol / Year: 2019
Title: An extensively glycosylated archaeal pilus survives extreme conditions.
Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Mark A B Kreutzberger / Zhangli Su / Guilherme A P de Oliveira / Tomasz Osinski / Nicholas Sherman / Frank DiMaio / Joseph S Wall / David ...Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Mark A B Kreutzberger / Zhangli Su / Guilherme A P de Oliveira / Tomasz Osinski / Nicholas Sherman / Frank DiMaio / Joseph S Wall / David Prangishvili / Mart Krupovic / Edward H Egelman /
Abstract: Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these ...Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these extracellular appendages to a very harsh environment. The pili, when removed from cells, resist digestion by trypsin or pepsin, and survive boiling in sodium dodecyl sulfate or 5 M guanidine hydrochloride. We used electron cryo-microscopy to determine the structure of these filaments at 4.1 Å resolution. An atomic model was built by combining the electron density map with bioinformatics without previous knowledge of the pilin sequence-an approach that should prove useful for assemblies where all of the components are not known. The atomic structure of the pilus was unusual, with almost one-third of the residues being either threonine or serine, and with many hydrophobic surface residues. While the map showed extra density consistent with glycosylation for only three residues, mass measurements suggested extensive glycosylation. We propose that this extensive glycosylation renders these filaments soluble and provides the remarkable structural stability. We also show that the overall fold of the archaeal pilin is remarkably similar to that of archaeal flagellin, establishing common evolutionary origins.
History
DepositionDec 6, 2018-
Header (metadata) releaseJan 23, 2019-
Map releaseMay 8, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nav
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nav
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0397.png

Downloads & links

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Map

FileDownload / File: emd_0397.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.127 / Movie #1: 0.127
Minimum - Maximum-0.15029839 - 0.3493753
Average (Standard dev.)0.00035732737 (±0.0065073087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.1500.3490.000

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Supplemental data

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Sample components

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Entire : Sulfolobus islandicus LAL14/1 Pilus

EntireName: Sulfolobus islandicus LAL14/1 Pilus
Components
  • Complex: Sulfolobus islandicus LAL14/1 Pilus
    • Protein or peptide: M9UD72

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Supramolecule #1: Sulfolobus islandicus LAL14/1 Pilus

SupramoleculeName: Sulfolobus islandicus LAL14/1 Pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sulfolobus islandicus LAL14/1 (archaea)

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Macromolecule #1: M9UD72

MacromoleculeName: M9UD72 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus LAL14/1 (archaea)
Molecular weightTheoretical: 12.681375 KDa
SequenceString:
LSGAVTALIL VIASVIIALV VVGFAFGLFG AFTGQGTVTQ VGTATLSAST GTLKVTLKNT GATTQVTGAI INGNAASVSG QVTISAGQS TYSISLGGIS SSTLQSLVGS TISLTLQLSN GQTVTVSAII TS

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: 6
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.0 sec. / Average electron dose: 48.0 e/Å2
Details: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2.
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 reconstructionApplied symmetry - Helical parameters - Δz: 4.94 Å
Applied symmetry - Helical parameters - Δ&Phi: 104.97 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software: (Name: SPIDER, RELION) / Details: MODEL:MAP FSC, D99 / Number images used: 181070
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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