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- EMDB-21653: Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21653 | |||||||||
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Title | Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the antiviral molecule DBT1 | |||||||||
![]() | HBV capsid in complex with the antiviral molecule DBT1. Icosahedral averaging imposed. | |||||||||
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![]() | capsid / antiviral / HBV / VIRUS LIKE PARTICLE | |||||||||
Function / homology | ![]() microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
![]() | Schlicksup C / Laughlin P | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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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 | ![]() | 190.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 22.8 KB | Display | ![]() |
Images | ![]() | 100.6 KB | ||
Masks | ![]() | 1000 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wfsMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | HBV capsid in complex with the antiviral molecule DBT1. Icosahedral averaging imposed. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Hepatitis B virus genotype D subtype adw
Entire | Name: ![]() |
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Components |
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-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 |
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-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 16.791104 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTAAALYRD ALESPEHASP HHTALRQAIL AWGDLMTLAT WVGTNLEDPA SRDLVVSYV NTNVGLKFRQ LLWFHISALT FGRETVLEYL VSFGVWIRTP PAYRPPNAPI LSTLPETTVV C UniProtKB: Capsid protein |
-Macromolecule #2: 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1...
Macromolecule | Name: 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide type: ligand / ID: 2 / Number of copies: 4 / Formula: U0A |
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Molecular weight | Theoretical: 453.534 Da |
Chemical component information | ![]() ChemComp-U0A: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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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 |
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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: ![]() |
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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 1-143 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation Coefficient |
Output model | ![]() PDB-6wfs: |