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- EMDB-1351: Structure and host cell interaction of SH1, a membrane-containing... -

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Basic information

Entry
Database: EMDB / ID: EMD-1351
TitleStructure and host cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus
Map dataCryoEM reconstruction of SH1 subviral particle VP36-.
Sample
  • Sample: SH1 subviral particle VP36-
  • Virus: Haloarcula phage SH1 (virus)
Biological speciesHaloarcula phage SH1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsJaalinoja HT / Roine E / Kivela H / Butcher SJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2008
Title: Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus.
Authors: Harri T Jäälinoja / Elina Roine / Pasi Laurinmäki / Hanna M Kivelä / Dennis H Bamford / Sarah J Butcher /
Abstract: The Archaea, and the viruses that infect them, are the least well understood of all of the three domains of life. They often grow in extreme conditions such as hypersaline lakes and sulfuric hot ...The Archaea, and the viruses that infect them, are the least well understood of all of the three domains of life. They often grow in extreme conditions such as hypersaline lakes and sulfuric hot springs. Only rare glimpses have been gained into the structures of archaeal viruses. Here, we report the subnanometer resolution structure of a recently isolated, hypersalinic, membrane-containing, euryarchaeal virus, SH1, in which different viral proteins can be localized. The results indicate that SH1 has a complex capsid formed from single beta-barrels, an important missing link in hypotheses on viral capsid protein evolution. Unusual, symmetry-mismatched spikes seem to play a role in host adsorption. They are connected to highly organized membrane proteins providing a platform for capsid assembly and potential machinery for host infection.
History
DepositionApr 2, 2007-
Header (metadata) releaseApr 2, 2007-
Map releaseMay 17, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5000
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1351.gif

Downloads & links

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Map

FileDownload / File: emd_1351.map.gz / Format: CCP4 / Size: 139 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryoEM reconstruction of SH1 subviral particle VP36-.
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level1: 5640.0 / Movie #1: 5000
Minimum - Maximum-15891.0 - 32443.0
Average (Standard dev.)304.646000000000015 (±3311.019999999999982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions421421421
Spacing421421421
CellA=B=C: 1178.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.82.82.8
M x/y/z421421421
origin x/y/z0.0000.0000.000
length x/y/z1178.8001178.8001178.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS421421421
D min/max/mean-15891.00032443.000304.646

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Supplemental data

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Sample components

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Entire : SH1 subviral particle VP36-

EntireName: SH1 subviral particle VP36-
Components
  • Sample: SH1 subviral particle VP36-
  • Virus: Haloarcula phage SH1 (virus)

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Supramolecule #1000: SH1 subviral particle VP36-

SupramoleculeName: SH1 subviral particle VP36- / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Haloarcula phage SH1

SupramoleculeName: Haloarcula phage SH1 / type: virus / ID: 1 / Name.synonym: SH1 subviral particle VP36- / NCBI-ID: 326574 / Sci species name: Haloarcula phage SH1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: SH1 subviral particle VP36-
Host (natural)Organism: Haloarcula hispanica (Halophile) / synonym: ARCHAEA
Virus shellShell ID: 1 / Name: capsid / Diameter: 800 Å / T number (triangulation number): 28

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2 / Details: 40 mM Tris-HCl pH 7.2, 0.75 M Na2SO4, 40 mM MgSO4
GridDetails: 400 mesh copper grid, Quantifoil R2/2 holey
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: EMBL design
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 94 K / Average: 93 K
DetailsLow dose conditions.
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 58
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.484 µm / Nominal defocus min: 0.733 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle, wiener factor 0.2
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: pft2, em3dr2, POR, P3DR / Number images used: 985

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