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- EMDB-21578: Cryo-EM of the Pyrobaculum arsenaticum pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-21578
TitleCryo-EM of the Pyrobaculum arsenaticum pilus
Map datacryo-EM of the P. arsenaticum pilus
Sample
  • Complex: Pyrobaculum arsenaticum pili
    • Protein or peptide: pilin
Keywordshelical symmetry / archaeal pilus / Type IV pilus / PROTEIN FIBRIL
Function / homologymembrane / Class III signal peptide-containing protein
Function and homology information
Biological speciesPyrobaculum arsenaticum (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang F / Baquero DP
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 Commun / Year: 2020
Title: The structures of two archaeal type IV pili illuminate evolutionary relationships.
Authors: Fengbin Wang / Diana P Baquero / Zhangli Su / Leticia C Beltran / David Prangishvili / Mart Krupovic / Edward H Egelman /
Abstract: We have determined the cryo-electron microscopic (cryo-EM) structures of two archaeal type IV pili (T4P), from Pyrobaculum arsenaticum and Saccharolobus solfataricus, at 3.8 Å and 3.4 Å ...We have determined the cryo-electron microscopic (cryo-EM) structures of two archaeal type IV pili (T4P), from Pyrobaculum arsenaticum and Saccharolobus solfataricus, at 3.8 Å and 3.4 Å resolution, respectively. This triples the number of high resolution archaeal T4P structures, and allows us to pinpoint the evolutionary divergence of bacterial T4P, archaeal T4P and archaeal flagellar filaments. We suggest that extensive glycosylation previously observed in T4P of Sulfolobus islandicus is a response to an acidic environment, as at even higher temperatures in a neutral environment much less glycosylation is present for Pyrobaculum than for Sulfolobus and Saccharolobus pili. Consequently, the Pyrobaculum filaments do not display the remarkable stability of the Sulfolobus filaments in vitro. We identify the Saccharolobus and Pyrobaculum T4P as host receptors recognized by rudivirus SSRV1 and tristromavirus PFV2, respectively. Our results illuminate the evolutionary relationships among bacterial and archaeal T4P filaments and provide insights into archaeal virus-host interactions.
History
DepositionMar 21, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0111
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0111
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w8u
  • Surface level: 0.0111
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6w8u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21578.png

Downloads & links

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Map

FileDownload / File: emd_21578.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of the P. arsenaticum 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: 0.0111 / Movie #1: 0.0111
Minimum - Maximum-0.027396144 - 0.054393522
Average (Standard dev.)0.000268633 (±0.002521249)
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 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0270.0540.000

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Supplemental data

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Sample components

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Entire : Pyrobaculum arsenaticum pili

EntireName: Pyrobaculum arsenaticum pili
Components
  • Complex: Pyrobaculum arsenaticum pili
    • Protein or peptide: pilin

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Supramolecule #1: Pyrobaculum arsenaticum pili

SupramoleculeName: Pyrobaculum arsenaticum pili / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pyrobaculum arsenaticum (archaea)

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Macromolecule #1: pilin

MacromoleculeName: pilin / type: protein_or_peptide / ID: 1 / Number of copies: 41 / Enantiomer: LEVO
Source (natural)Organism: Pyrobaculum arsenaticum (archaea)
Molecular weightTheoretical: 14.49064 KDa
SequenceString:
MTSLEIAIIV AIVLVIAIAV GWYLYTTFAA AGQQTGLTAT KATIYVTKDG NVYLNVTLVP QGAAQVAISS IEVAGVSIPC TSSNLVKAP GEYVIELSSV SVSVGQVLTG RIVLASGAIS PFTATVVAAD HVPSTENKLC SSQ

UniProtKB: Class III signal peptide-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: 6
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 44.0 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 reconstructionApplied symmetry - Helical parameters - Δz: 5.26051 Å
Applied symmetry - Helical parameters - Δ&Phi: 101.691 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Number images used: 210341
Startup modelType of model: OTHER
Details: averaged cylinder using all segments, with random azimuthal angles
Final angle assignmentType: NOT APPLICABLE

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