National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI144022
United States
Citation
Journal: J Biol Chem / Year: 2023 Title: Structure of the Hepatitis B virus capsid quasi-6-fold with a trapped C-terminal domain reveals capsid movements associated with domain exit. Authors: Christine Kim / Christopher J Schlicksup / Carolina Pérez-Segura / Jodi A Hadden-Perilla / Joseph Che-Yen Wang / Adam Zlotnick / Abstract: Many viruses undergo transient conformational change to surveil their environments for receptors and host factors. In Hepatitis B virus (HBV) infection, after the virus enters the cell, it is ...Many viruses undergo transient conformational change to surveil their environments for receptors and host factors. In Hepatitis B virus (HBV) infection, after the virus enters the cell, it is transported to the nucleus by interaction of the HBV capsid with an importin α/β complex. The interaction between virus and importins is mediated by nuclear localization signals on the capsid protein's C-terminal domain (CTD). However, CTDs are located inside the capsid. In this study, we asked where does a CTD exit the capsid, are all quasi-equivalent CTDs created equal, and does the capsid structure deform to facilitate CTD egress from the capsid? Here, we used Impβ as a tool to trap transiently exposed CTDs and examined this complex by cryo-electron microscopy. We examined an asymmetric reconstruction of a T = 4 icosahedral capsid and a focused reconstruction of a quasi-6-fold vertex (3.8 and 4.0 Å resolution, respectively). Both approaches showed that a subset of CTDs extended through a pore in the center of the quasi-6-fold complex. CTD egress was accompanied by enlargement of the pore and subtle changes in quaternary and tertiary structure of the quasi-6-fold. When compared to molecular dynamics simulations, structural changes were within the normal range of capsid flexibility. Although pore diameter was enlarged in the Impβ-bound reconstruction, simulations indicate that CTD egress does not exclusively depend on enlarged pores. In summary, we find that HBV surveillance of its environment by transient exposure of its CTD requires only modest conformational change of the capsid.
Model: Talos Arctica / Image courtesy: FEI Company
+
Image processing
Particle selection
Number selected: 31166
Startup model
Type of model: OTHER Details: An initial de novo model with C1 symmetry was generated using Relion.
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1154892
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classification
Software - Name: RELION Details: Symmetry expansion and alignment was applied to the refined I2 map for focused reconstruction. 1,730,160 quasi-6-fold vertices (referred as hexamers) were extracted. The particles were used ...Details: Symmetry expansion and alignment was applied to the refined I2 map for focused reconstruction. 1,730,160 quasi-6-fold vertices (referred as hexamers) were extracted. The particles were used to generate a new initial hexamer model de novo with C1 symmetry, which was used as a reference map for subsequent 3D classification.
FSC plot (resolution estimation)
-
Atomic model buiding 1
Details
A hexamer model was flexibly fitted into the hexamer maps using Alphafold, ISOLDE, PHENIX, and Coot.
Refinement
Protocol: RIGID BODY FIT
Output model
PDB-8ghs: Empty HBV Cp183 capsid with importin-beta, subparticle reconstruction at 2-fold location
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi