+Open data
-Basic information
Entry | Database: PDB / ID: 8c0o | ||||||||||||
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Title | African cichlid nackednavirus capsid at pH 5.5 | ||||||||||||
Components | C protein | ||||||||||||
Keywords | VIRAL PROTEIN / T=3 / Capsid protein | ||||||||||||
Function / homology | C protein Function and homology information | ||||||||||||
Biological species | African cichlid nackednavirus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Pfister, S. / Rabl, J. / Boehringer, D. / Meier, B.H. | ||||||||||||
Funding support | European Union, Switzerland, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural conservation of HBV-like capsid proteins over hundreds of millions of years despite the shift from non-enveloped to enveloped life-style. Authors: Sara Pfister / Julius Rabl / Thomas Wiegand / Simone Mattei / Alexander A Malär / Lauriane Lecoq / Stefan Seitz / Ralf Bartenschlager / Anja Böckmann / Michael Nassal / Daniel Boehringer / Beat H Meier / Abstract: The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV ...The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV acquired an envelope during evolution, nackednaviruses remained non-enveloped. We report the capsid structure of the African cichlid nackednavirus (ACNDV), determined by cryo-EM at 3.7 Å resolution. This enables direct comparison with the known capsid structures of HBV and duck HBV, prototypic representatives of the mammalian and avian lineages of the enveloped Hepadnaviridae, respectively. The sequence identity with HBV is 24% and both the ACNDV capsid protein fold and the capsid architecture are very similar to those of the Hepadnaviridae and HBV in particular. Acquisition of the hepadnaviral envelope was thus not accompanied by a major change in capsid structure. Dynamic residues at the spike tip are tentatively assigned by solid-state NMR, while the C-terminal domain is invisible due to dynamics. Solid-state NMR characterization of the capsid structure reveals few conformational differences between the quasi-equivalent subunits of the ACNDV capsid and an overall higher capsid structural disorder compared to HBV. Despite these differences, the capsids of ACNDV and HBV are structurally highly similar despite the 400 million years since their separation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c0o.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8c0o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8c0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c0o_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 8c0o_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 8c0o_validation.xml.gz | 440.1 KB | Display | |
Data in CIF | 8c0o_validation.cif.gz | 704.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/8c0o ftp://data.pdbj.org/pub/pdb/validation_reports/c0/8c0o | HTTPS FTP |
-Related structure data
Related structure data | 16371MC 8aacC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 19851.234 Da / Num. of mol.: 180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African cichlid nackednavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S9H6T3 |
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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: African cichlid nackednavirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 3.57 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: African cichlid nackednavirus | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pRSF_T7 | |||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||
Natural host | Organism: Ophthalmotilapia ventralis | |||||||||||||||||||||||||
Virus shell | Name: capsid / Diameter: 230 nm / Triangulation number (T number): 3 | |||||||||||||||||||||||||
Buffer solution | pH: 5.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The protein concentration is approx. 0.1-0.5 mg/mL | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 166000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 55 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 5362 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 215225 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77129 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL Details: One protein chain was manually built in Coot. The chain was multiplied to give 180 chains, which were arranged as an icosahedral capsid. The capsid was refined with phenix and Isolde. |