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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0050 | |||||||||
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Title | DNA-devoid HCIV-1 virus particle | |||||||||
![]() | This map corresponds to DNA-devoid HCIV-1 particles. A cut through shows the lack of DNA and the unexpanded membrane vesicle. To better distinguish the membrane it is advisable to filter to 10 Ang. | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.9 Å | |||||||||
![]() | Santos-Perez I / Charro D / Gil-Carton D / Azkargorta M / Elortza F / Bamford DH / Oksanen HM / Abrescia NGA | |||||||||
![]() | ![]() Title: Structural basis for assembly of vertical single β-barrel viruses. Authors: Isaac Santos-Pérez / Diego Charro / David Gil-Carton / Mikel Azkargorta / Felix Elortza / Dennis H Bamford / Hanna M Oksanen / Nicola G A Abrescia / ![]() ![]() Abstract: The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The ...The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs. | |||||||||
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 | ![]() | 201.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 176.1 KB | ||
Others | ![]() ![]() | 170.7 MB 170.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 435.5 KB | Display | ![]() |
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Full document | ![]() | 434.6 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0072C ![]() 0073C ![]() 0131C ![]() 0172C ![]() 0174C ![]() 6h82C ![]() 6h9cC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | This map corresponds to DNA-devoid HCIV-1 particles. A cut through shows the lack of DNA and the unexpanded membrane vesicle. To better distinguish the membrane it is advisable to filter to 10 Ang. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_0050_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_0050_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Haloarcula californiae ATCC 33799
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Haloarcula californiae ATCC 33799
Supramolecule | Name: Haloarcula californiae ATCC 33799 / type: virus / ID: 1 / Parent: 0 / Details: Haloarcula californiae icosahedral virus - 1 / NCBI-ID: 662475 / Sci species name: Haloarcula californiae ATCC 33799 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 800.0 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 | 1.2 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-26 / Number grids imaged: 1 / Number real images: 3218 / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |