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- EMDB-3110: Insight into the assembly of viruses with vertical single beta-ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-3110
TitleInsight into the assembly of viruses with vertical single beta-barrel major capsid proteins
Map datasub-tomogram averaging of five-fold vertices with spike-OFF. This has been then gaussian filterd to 15 Ang
Sample
  • Sample: Haloarcula hispanica icosahedral virus 2 (HHIV-2)
  • Virus: Haloarcula hispanica icosahedral virus 2
Keywordsarchaeal virus / assembly / spike complex-OFF
Biological speciesHaloarcula hispanica icosahedral virus 2
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsGil-Carton D / Jaakkola ST / Charro D / Peralta B / Castano-Diez D / Oksanen HM / Bamford DH / Abrescia NG
CitationJournal: Structure / Year: 2015
Title: Insight into the Assembly of Viruses with Vertical Single β-barrel Major Capsid Proteins.
Authors: David Gil-Carton / Salla T Jaakkola / Diego Charro / Bibiana Peralta / Daniel Castaño-Díez / Hanna M Oksanen / Dennis H Bamford / Nicola G A Abrescia /
Abstract: Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of ...Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of life. Here, using biochemical and cryo-electron microscopy techniques, we solved the structure of euryarchaeal, halophilic, internal membrane-containing Haloarcula hispanica icosahedral virus 2 (HHIV-2). We show that the density of the two major capsid proteins (MCPs) recapitulates vertical single β-barrel proteins and that disulfide bridges stabilize the capsid. Below, ordered density is visible close to the membrane and at the five-fold vertices underneath the host-interacting vertex complex underpinning membrane-protein interactions. The HHIV-2 structure exemplifies the division of conserved architectural elements of a virion, such as the capsid, from those that evolve rapidly due to selective environmental pressure such as host-recognizing structures. We propose that in viruses with two vertical single β-barrel MCPs the vesicle is indispensable, and membrane-protein interactions serve as protein-railings for guiding the assembly.
History
DepositionJul 28, 2015-
Header (metadata) releaseAug 26, 2015-
Map releaseSep 9, 2015-
UpdateOct 14, 2015-
Current statusOct 14, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB_figure_...

Downloads & links

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Map

FileDownload / File: emd_3110.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsub-tomogram averaging of five-fold vertices with spike-OFF. This has been then gaussian filterd to 15 Ang
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.2 Å/pix.
x 64 pix.
= 460.8 Å		7.2 Å/pix.
x 64 pix.
= 460.8 Å		7.2 Å/pix.
x 64 pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-2.31878757 - 3.08878613
Average (Standard dev.)-0.07043877 (±0.64419353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 460.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.27.27.2
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-2.3193.089-0.070

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Supplemental data

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Sample components

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Entire : Haloarcula hispanica icosahedral virus 2 (HHIV-2)

EntireName: Haloarcula hispanica icosahedral virus 2 (HHIV-2)
Components
  • Sample: Haloarcula hispanica icosahedral virus 2 (HHIV-2)
  • Virus: Haloarcula hispanica icosahedral virus 2

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Supramolecule #1000: Haloarcula hispanica icosahedral virus 2 (HHIV-2)

SupramoleculeName: Haloarcula hispanica icosahedral virus 2 (HHIV-2) / type: sample / ID: 1000
Details: While the sample is a virus, the subtomogram averaged map corresponds to the components forming the five-fold vertices with the spike complex OFF.
Oligomeric state: Icosahedral Virus / Number unique components: 1

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Supramolecule #1: Haloarcula hispanica icosahedral virus 2

SupramoleculeName: Haloarcula hispanica icosahedral virus 2 / type: virus / ID: 1 / Details: HHIV-2 is a lipid-containing virus / NCBI-ID: 1154689 / Sci species name: Haloarcula hispanica icosahedral virus 2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloarcula hispanica (Halophile) / synonym: ARCHAEA
Virus shellShell ID: 1 / Name: SPIKE COMPLEX-OFF

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.2
Details: 20 mM Tris-HCl [pH 7.2], 20 mM MgCl2, 10 mM CaCl2, and 0.5 M NaCl
GridDetails: 200-mesh Quantifoil R 3.5/1 holey-carbon grids
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2200FSC
TemperatureMin: 80 K / Max: 103 K / Average: 99 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV
DateJun 17, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Average electron dose: 80 e/Å2
Details: Single-axis tilt series collection under low-dose conditions was automated with SerialEM data acquisition software.
Bits/pixel: 32
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 42147 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 30000
Sample stageSpecimen holder: Ultra-high tilt cryotransfer holder (Model 914 High tilt Tomography Holder, GATAN)
Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 °

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Image processing

DetailsThe subtomograms were selected using Dynamo with automatic selection of the five-fold vertices. The extracted vertices were then submitted to a multireference alignment procedure with 5 classes.
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: OTHER / Software - Name: IMOD, Dynamo / Number subtomograms used: 1334
CTF correctionDetails: TOMOCTF method
Final 3D classificationNumber classes: 5

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