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- EMDB-3109: Insight into the assembly of viruses with vertical single beta-ba... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3109 | |||||||||
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Title | Insight into the assembly of viruses with vertical single beta-barrel major capsid proteins | |||||||||
![]() | Reconstruction 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. | |||||||||
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![]() | archaeal virus | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||
![]() | Gil-Carton D / Jaakkola ST / Charro D / Peralta B / Castano-Diez D / Oksanen HM / Bamford DH / Abrescia NG | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 147.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.3 KB 13.3 KB | Display Display | ![]() |
Images | ![]() | 465 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 254.8 KB | Display | ![]() |
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Full document | ![]() | 253.9 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction 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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Haloarcula hispanica icosahedral virus 2 (HHIV-2)
Entire | Name: Haloarcula hispanica icosahedral virus 2 (HHIV-2) |
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Components |
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-Supramolecule #1000: Haloarcula hispanica icosahedral virus 2 (HHIV-2)
Supramolecule | Name: 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
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: VP4-VP7 / Diameter: 740 Å / T number (triangulation number): 28 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.2 Details: 20 mM Tris-HCl [pH 7.2], 20 mM MgCl2, 10 mM CaCl2, and 0.5 M NaCl |
Grid | Details: 200-mesh Quantifoil R 2/1 holey-carbon grids |
Vitrification | Cryogen 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
Microscope | JEOL 2200FSC |
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Temperature | Min: 80 K / Max: 103 K / Average: 99 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Specialist optics | Energy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV |
Date | Oct 27, 2014 |
Image recording | Category: 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 beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated 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 stage | Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: micrograph |
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Final reconstruction | Applied 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 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | We 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). |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | We 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). |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 3
Initial model | PDB ID: Chain - Chain ID: Q |
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Software | Name: ![]() |
Details | We 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). |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 4
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | The trimer was manually fitted into density using COOT |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 5
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | The trimer was manually fitted into density using COOT. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |