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- EMDB-1498: Vertex reconstruction of SH1 spike -

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Basic information

Entry
Database: EMDB / ID: EMD-1498
TitleVertex reconstruction of SH1 spike
Map dataspike
Sample
  • Sample: SH1 virus, reconstruction of the non-icosahedrally symmetric spikes on the vertices
  • Virus: Haloarcula phage SH1 (virus)
Keywordsarchaea / virus / SH1 / spike / infection / adsorption
Biological speciesHaloarcula phage SH1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 34.0 Å
AuthorsJaalinoja HT / Roine E / Laurinmaki P / Kivela HM / Bamford DH / 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
DepositionMar 17, 2008-
Header (metadata) releaseMar 18, 2008-
Map releaseMar 31, 2009-
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: 1000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1498.png

Downloads & links

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Map

FileDownload / File: emd_1498.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationspike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 150 pix.
= 420. Å		2.8 Å/pix.
x 150 pix.
= 420. Å		2.8 Å/pix.
x 150 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.2.82.82.8
CCP4 map header2.82.82.8
EM Navigator Movie #1222
Density

Histogram

Histogram (log scale)
Contour Level1: 526.0 / Movie #1: 1000
Minimum - Maximum-1553.509999999999991 - 6843.880000000000109
Average (Standard dev.)83.340900000000005 (±443.437999999999988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 420 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-1553.5086843.88383.341

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Supplemental data

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Sample components

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Entire : SH1 virus, reconstruction of the non-icosahedrally symmetric spik...

EntireName: SH1 virus, reconstruction of the non-icosahedrally symmetric spikes on the vertices
Components
  • Sample: SH1 virus, reconstruction of the non-icosahedrally symmetric spikes on the vertices
  • Virus: Haloarcula phage SH1 (virus)

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Supramolecule #1000: SH1 virus, reconstruction of the non-icosahedrally symmetric spik...

SupramoleculeName: SH1 virus, reconstruction of the non-icosahedrally symmetric spikes on the vertices
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 / NCBI-ID: 326574 / Sci species name: Haloarcula phage SH1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: SH1
Host (natural)Organism: Haloarcula hispanica (Halophile) / synonym: ARCHAEA

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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: 150-500 mM NaCl, 10mM MgCl2, 10 M MgSO4, 5 mM KCl, 3 mM CaCl2, 40 mM Tris-HCl pH 7.2
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: 169
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: 2.5 µm / Nominal defocus min: 0.7 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 micrograph
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, EMAN, BSoft / Details: Vertex reconstruction. / Number images used: 10196
Final two d classificationNumber classes: 548

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