ArticleBio-protocol2023
Protein Structure Predictions, Atomic Model Building, and Validation Using a Cryo-EM Density Map from Hepatitis B Virus Spherical Subviral Particle.
Article in Bio-protocol, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
4 citing papers in PubMed.
- Negative cooperativity drives activity of capsid-directed antivirals against hepatitis B virus.Science advances · 2026Article
- Cryo-EM structures of HBV capsids from human cells at near-atomic resolution.Structure (London, England : 1993) · 2026Article
- The CD4 T cell-independent IgG response during persistent virus infection favors emergence of neutralization-escape variants.bioRxiv : the preprint server for biology · 2024Article
- Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages.Bio-protocol · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Hepatitis B virus (HBV) infection is a global public health concern. During chronic infection, the HBV small-surface antigen is expressed in large excess as non-infectious spherical subviral particles (SVPs), which possess strong immunogenicity. To date, attempts at understanding the structure of HBV spherical SVP have been restricted to 12-30 Å with contradictory conclusions regarding its architecture. We have used cryo-electron microscopy (cryo-EM) and 3D image reconstruction to solve the HBV spherical SVP to 6.3 Å. Here, we present an extended protocol on combining AlphaFold2 prediction with a moderate-resolution cryo-EM density map to build a reliable 3D model. This protocol utilizes multiple software packages that are routinely used in the cryo-EM community. The workflow includes 3D model prediction, model evaluation, rigid-body fitting, flexible fitting, real-space refinement, model validation, and model adjustment. Finally, the described protocol can also be applied to high-resolution cryo-EM datasets (2-4 Å).
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Registered trials
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