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- EMDB-40048: Empty HBV Cp183 capsid with importin-beta -

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Basic information

Entry
Database: EMDB / ID: EMD-40048
TitleEmpty HBV Cp183 capsid with importin-beta
Map dataCryo-EM model of HBV in complex with Importin-beta
Sample
  • Complex: Reassembled HBV empty Cp183 capsid with importin-beta
KeywordsHBV / Cp183 / Importin-beta / VIRUS LIKE PARTICLE
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKim C / Schlicksup CJ / Hadden-Perilla JA / Wang JC-Y / Zlotnick A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144022 United States
CitationJournal: 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.
History
DepositionMar 10, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40048.png

Downloads & links

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Map

FileDownload / File: emd_40048.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM model of HBV in complex with Importin-beta
Voxel sizeX=Y=Z: 0.97 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.040927235 - 0.07712007
Average (Standard dev.)0.00027502456 (±0.004329155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 496.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map2

Fileemd_40048_half_map_1.map
AnnotationHalf-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map1

Fileemd_40048_half_map_2.map
AnnotationHalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Reassembled HBV empty Cp183 capsid with importin-beta

EntireName: Reassembled HBV empty Cp183 capsid with importin-beta
Components
  • Complex: Reassembled HBV empty Cp183 capsid with importin-beta

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Supramolecule #1: Reassembled HBV empty Cp183 capsid with importin-beta

SupramoleculeName: Reassembled HBV empty Cp183 capsid with importin-beta / type: complex / ID: 1 / Parent: 0 / Details: Core protein Cp183 expressed in E coli
Source (natural)Organism: Hepatitis B virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 0.15 M NaCl, 20 mM Tris-HCl pH 7.5, and 10 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsEmpty HBV capsid : Importin-beta sample at 1:205

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 31166
Startup modelType of model: OTHER
Details: An initial de novo model with C1 symmetry was generated using Relion.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 29006
FSC plot (resolution estimation)

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