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- EMDB-3109: Insight into the assembly of viruses with vertical single beta-ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-3109
TitleInsight into the assembly of viruses with vertical single beta-barrel major capsid proteins
Map dataReconstruction of Haloarcula hispanica icosahedral virus 2 (HHIV-2. The recommended contour level (threshold) suggested is for visualizing the capsid in Chimera. Lower thresholds are required for example to display the spikes.
Sample
  • Sample: Haloarcula hispanica icosahedral virus 2 (HHIV-2)
  • Virus: Haloarcula hispanica icosahedral virus 2
Keywordsarchaeal virus
Biological speciesHaloarcula hispanica icosahedral virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 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: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.045
  • 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_3109.map.gz / Format: CCP4 / Size: 157 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Haloarcula hispanica icosahedral virus 2 (HHIV-2. The recommended contour level (threshold) suggested is for visualizing the capsid in Chimera. Lower thresholds are required for example to display the spikes.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 348 pix.
= 1183.2 Å		3.4 Å/pix.
x 348 pix.
= 1183.2 Å		3.4 Å/pix.
x 348 pix.
= 1183.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.06295919 - 0.22115071
Average (Standard dev.)0.01261325 (±0.04221636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions348348348
Spacing348348348
CellA=B=C: 1183.2001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.43.43.4
M x/y/z348348348
origin x/y/z0.0000.0000.000
length x/y/z1183.2001183.2001183.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS348348348
D min/max/mean-0.0630.2210.013

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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 / 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: VP4-VP7 / Diameter: 740 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

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 2/1 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: 15.0 eV
DateOct 27, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 900 / Average electron dose: 10 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 90200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: OTHER / Software - Name: XMIPP / Details: 11 Ang FSC at 0.143 cut-off / Number images used: 4875

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Atomic model buiding 1

Initial modelPDB ID:

3zn5

SoftwareName: COOT
DetailsWe used the VP17 and VP16 pdbs previously fitted into the P23-77 cryo-EM maps by Rissanen et al (2013) Structure. We selected from the above fitting as rigid body a VP17 with two adjacent VP16. Then, we fitted as rigid body the VP16-VP17-VP16 oligomer in our map into capsomer 5 (please see our publication Figure 4D).
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

3zmn

SoftwareName: COOT
DetailsWe used the VP17 and VP16 pdbs previously fitted into the P23-77 cryo-EM maps by Rissanen et al (2013) Structure. We selected from the above fitting as rigid body a VP17 with two adjacent VP16. Then, we fitted as rigid body the VP16-VP17-VP16 oligomer in our map into capsomer 5 using the COOT command 'Rigid body fit zone' (please see our publication Figure 4D).
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 3

Initial modelPDB ID:

3j31


Chain - Chain ID: Q
SoftwareName: COOT
DetailsWe first generated the pentameric structure correspondingto the STIV map - Veesler et al (2013) PNAS- and then used the pentamer for rigid-body fitting using the COOT command 'Rigid body fit zone' in our cryo-EM density (please see Figure 7).
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 4

Initial modelPDB ID:

2poh

SoftwareName: COOT
DetailsThe trimer was manually fitted into density using COOT
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 5

Initial modelPDB ID:

4d1g

SoftwareName: COOT
DetailsThe trimer was manually fitted into density using COOT.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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