+Open data
-Basic information
Entry | Database: PDB / ID: 6z8d | ||||||
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Title | Human Picobirnavirus CP VLP | ||||||
Components | Capsid protein precursor | ||||||
Keywords | VIRUS LIKE PARTICLE / Human Picobirnavirus / CryoEM / assembly / capsid protein | ||||||
Function / homology | : / : / Picobirnavirus, Capsid protein / T=3 icosahedral viral capsid / Capsid protein precursor Function and homology information | ||||||
Biological species | Human picobirnavirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å | ||||||
Authors | Ortega-Esteban, A. / Mata, C.P. / Rodriguez-Espinosa, M.J. / Luque, D. / Irigoyen, N. / Rodriguez, J.M. / de Pablo, P.J. / Caston, J.R. | ||||||
Funding support | Spain, 1items
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Citation | Journal: J Virol / Year: 2020 Title: Cryo-electron Microscopy Structure, Assembly, and Mechanics Show Morphogenesis and Evolution of Human Picobirnavirus. Authors: Álvaro Ortega-Esteban / Carlos P Mata / María J Rodríguez-Espinosa / Daniel Luque / Nerea Irigoyen / Javier M Rodríguez / Pedro J de Pablo / José R Castón / Abstract: Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and ...Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and replication. This ubiquitous capsid remains structurally undisturbed throughout the viral cycle, isolating the genome to avoid triggering host defense mechanisms. Human picobirnavirus (hPBV) is a dsRNA virus frequently associated with gastroenteritis, although its pathogenicity is yet undefined. Here, we report the cryo-electron microscopy (cryo-EM) structure of hPBV at 2.6-Å resolution. The capsid protein (CP) is arranged in a single-shelled, ∼380-Å-diameter T=1 capsid with a rough outer surface similar to that of dsRNA mycoviruses. The hPBV capsid is built of 60 quasisymmetric CP dimers (A and B) stabilized by domain swapping, and only the CP-A N-terminal basic region interacts with the packaged nucleic acids. hPBV CP has an α-helical domain with a fold similar to that of fungal partitivirus CP, with many domain insertions in its C-terminal half. In contrast to dsRNA mycoviruses, hPBV has an extracellular life cycle phase like complex reoviruses, which indicates that its own CP probably participates in cell entry. Using an reversible assembly/disassembly system of hPBV, we isolated tetramers as possible assembly intermediates. We used atomic force microscopy to characterize the biophysical properties of hPBV capsids with different cargos (host nucleic acids or proteins) and found that the CP N-terminal segment not only is involved in nucleic acid interaction/packaging but also modulates the mechanical behavior of the capsid in conjunction with the cargo. Despite intensive study, human virus sampling is still sparse, especially for viruses that cause mild or asymptomatic disease. Human picobirnavirus (hPBV) is a double-stranded-RNA virus, broadly dispersed in the human population, but its pathogenicity is uncertain. Here, we report the hPBV structure derived from cryo-electron microscopy (cryo-EM) and reconstruction methods using three capsid protein variants (of different lengths and N-terminal amino acid compositions) that assemble as virus-like particles with distinct properties. The hPBV near-atomic structure reveals a quasisymmetric dimer as the structural subunit and tetramers as possible assembly intermediates that coassemble with nucleic acids. Our structural studies and atomic force microscopy analyses indicate that hPBV capsids are potentially excellent nanocages for gene therapy and targeted drug delivery in humans. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6z8d.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z8d.ent.gz | 149.6 KB | Display | PDB format |
PDBx/mmJSON format | 6z8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z8d_validation.pdf.gz | 342.4 KB | Display | wwPDB validaton report |
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Full document | 6z8d_full_validation.pdf.gz | 346.4 KB | Display | |
Data in XML | 6z8d_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 6z8d_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/6z8d ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z8d | HTTPS FTP |
-Related structure data
Related structure data | 11115MC 6z8eC 6z8fC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 62084.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human picobirnavirus / Gene: Segment-1, ORF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q50LE5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human picobirnavirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Source (natural) | Organism: Human picobirnavirus | ||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pRSET | ||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||
Virus shell | Name: Capsid Protein / Diameter: 380 nm / Triangulation number (T number): 1 | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 306 nm / Calibrated defocus max: 4040 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.56 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2360 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102722 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2VF1 Accession code: 2VF1 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
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