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- EMDB-20477: Attachment of STIV to Sulfolobus pili -

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Basic information

Entry
Database: EMDB / ID: EMD-20477
TitleAttachment of STIV to Sulfolobus pili
Map dataAttachment of Sulfolobus Turreted Icosahedral Virus (STIV) to Sulfolobus pili
Sample
  • Virus: Sulfolobus turreted icosahedral virus 1
Biological speciesSulfolobus turreted icosahedral virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsLawrence CM / Young MA / Hartman RA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1342876 United States
National Science Foundation (NSF, United States)1413534 United States
CitationJournal: Structure / Year: 2019
Title: The Molecular Mechanism of Cellular Attachment for an Archaeal Virus.
Authors: Ross Hartman / Brian J Eilers / Daniel Bollschweiler / Jacob H Munson-McGee / Harald Engelhardt / Mark J Young / C Martin Lawrence /
Abstract: Sulfolobus turreted icosahedral virus (STIV) is a model archaeal virus and member of the PRD1-adenovirus lineage. Although STIV employs pyramidal lysis structures to exit the host, knowledge of the ...Sulfolobus turreted icosahedral virus (STIV) is a model archaeal virus and member of the PRD1-adenovirus lineage. Although STIV employs pyramidal lysis structures to exit the host, knowledge of the viral entry process is lacking. We therefore initiated studies on STIV attachment and entry. Negative stain and cryoelectron micrographs showed virion attachment to pili-like structures emanating from the Sulfolobus host. Tomographic reconstruction and sub-tomogram averaging revealed pili recognition by the STIV C381 turret protein. Specifically, the triple jelly roll structure of C381 determined by X-ray crystallography shows that pilus recognition is mediated by conserved surface residues in the second and third domains. In addition, the STIV petal protein (C557), when present, occludes the pili binding site, suggesting that it functions as a maturation protein. Combined, these results demonstrate a role for the namesake STIV turrets in initial cellular attachment and provide the first molecular model for viral attachment in the archaeal domain of life.
History
DepositionJul 17, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseAug 28, 2019-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 80
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 80
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20477.png

Downloads & links

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Map

FileDownload / File: emd_20477.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAttachment of Sulfolobus Turreted Icosahedral Virus (STIV) to Sulfolobus pili
Voxel sizeX=Y=Z: 4.5 Å
Density
Contour LevelBy AUTHOR: 80 / Movie #1: 80
Minimum - Maximum-128.2953 - 366.95636
Average (Standard dev.)0.28934854 (±5.7283134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-399-29101
Dimensions13891771401
Spacing17711389401
CellA: 7969.5 Å / B: 6250.5 Å / C: 1804.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.54.54.5
M x/y/z17711389401
origin x/y/z0.0000.0000.000
length x/y/z7969.5006250.5001804.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ254265109
MAP C/R/S123
start NC/NR/NS-29-399101
NC/NR/NS17711389401
D min/max/mean-128.295366.9560.289

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Supplemental data

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Sample components

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Entire : Sulfolobus turreted icosahedral virus 1

EntireName: Sulfolobus turreted icosahedral virus 1
Components
  • Virus: Sulfolobus turreted icosahedral virus 1

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Supramolecule #1: Sulfolobus turreted icosahedral virus 1

SupramoleculeName: Sulfolobus turreted icosahedral virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 269145 / Sci species name: Sulfolobus turreted icosahedral virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Saccharolobus solfataricus P2 (archaea) / Strain: P2^3
Virus shellShell ID: 1 / Diameter: 740.0 Å / T number (triangulation number): 31

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 2.5 / Component - Concentration: 5.0 mM / Component - Formula: C6H8O7 / Component - Name: Citric Acid
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK III
Details1 ml S. solfactaricus cells at approximately 5E10^8 cells/ml was combined with 100 ul of 1.88 mg/ml virus and incubated for 20 minutes at 80C. Unbound virus was removed by centrifugation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 7
ExtractionNumber tomograms: 1 / Number images used: 3 / Software - Name: PEET
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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