- EMDB-21655: Focused asymmetric reconstruction of a pentamer of capsid protein... -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-21655
Title
Focused asymmetric reconstruction of a pentamer of capsid protein subunits surrounding an icosahedral 5-fold axis from a Heptatis B virus capsid in complex with an antiviral molecule
Map data
A focused asymmetric reconstruction of a pentamer of protein subunits from a Heptatitis B virus capsid in complex with an antiviral. The pentamer is located on the icosahedral 5-fold symmetry axis.
Sample
Virus: Hepatitis B virus genotype D subtype adw
Biological species
Hepatitis B virus genotype D subtype adw
Method
single particle reconstruction / cryo EM / Resolution: 3.7 Å
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI067417
United States
Citation
Journal: ACS Chem Biol / Year: 2020 Title: Local Stabilization of Subunit-Subunit Contacts Causes Global Destabilization of Hepatitis B Virus Capsids. Authors: Christopher John Schlicksup / Patrick Laughlin / Steven Dunkelbarger / Joseph Che-Yen Wang / Adam Zlotnick / Abstract: Development of antiviral molecules that bind virion is a strategy that remains in its infancy, and the details of their mechanisms are poorly understood. Here we investigate the behavior of DBT1, a ...Development of antiviral molecules that bind virion is a strategy that remains in its infancy, and the details of their mechanisms are poorly understood. Here we investigate the behavior of DBT1, a dibenzothiazepine that specifically interacts with the capsid protein of hepatitis B virus (HBV). We found that DBT1 stabilizes protein-protein interaction, accelerates capsid assembly, and can induce formation of aberrant particles. Paradoxically, DBT1 can cause preformed capsids to dissociate. These activities may lead to (i) assembly of empty and defective capsids, inhibiting formation of new virus, and (ii) disruption of mature viruses, which are metastable, to inhibit new infection. Using cryo-electron microscopy, we observed that DBT1 led to asymmetric capsids where well-defined DBT1 density was bound at all intersubunit contacts. These results suggest that DBT1 can support assembly by increasing buried surface area but induce disassembly of metastable capsids by favoring asymmetry to induce structural defects.
History
Deposition
Apr 3, 2020
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Header (metadata) release
Jun 3, 2020
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Map release
Jun 3, 2020
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Update
Jul 1, 2020
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Current status
Jul 1, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_21655.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
A focused asymmetric reconstruction of a pentamer of protein subunits from a Heptatitis B virus capsid in complex with an antiviral. The pentamer is located on the icosahedral 5-fold symmetry axis.
Supramolecule #1: Hepatitis B virus genotype D subtype adw
Supramolecule
Name: Hepatitis B virus genotype D subtype adw / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10419 / Sci species name: Hepatitis B virus genotype D subtype adw / Sci species strain: isolate United Kingdom/adyw/1979 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host system
Organism: Escherichia coli (E. coli)
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
10 mg/mL
Buffer
pH: 7.5 Component:
Concentration
Formula
Name
50.0 mM
C8H18N2O4S
HEPES
300.0 mM
NaCl
Sodium Chloride
Grid
Details: unspecified
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK III
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 679 / Average electron dose: 33.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 24823
CTF correction
Software - Name: CTFFIND (ver. 4.1)
Startup model
Type of model: NONE / Details: A spherical volume with a diameter of 35 nm
Final reconstruction
Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Software - details: Automated B-factor Sharpening Details: The particle number represents symmetry expanded subparticles, generated using "relion_symmetry_expand" following an icosahedral reconstruction. Number images used: 392736
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