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- EMDB-40049: empty HBV Cp183 capsid with importin-beta, subparticle reconstruc... -

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Basic information

Entry
Database: EMDB / ID: EMD-40049
Titleempty HBV Cp183 capsid with importin-beta, subparticle reconstruction at 2fold location
Map dataempty HBV Cp183 capsid with importin-beta, subparticle reconstruction at 2fold location
Sample
  • Complex: Reassembled HBV empty Cp183 capsid with importin-beta
    • Protein or peptide: Capsid protein
KeywordsHBV / Cp183 / Importin-beta / VIRAL PROTEIN
Function / homology
Function and homology information


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
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40049.png

Downloads & links

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Map

FileDownload / File: emd_40049.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationempty HBV Cp183 capsid with importin-beta, subparticle reconstruction at 2fold location
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.94 Å/pix.
x 120 pix.
= 232.8 Å		1.94 Å/pix.
x 120 pix.
= 232.8 Å		1.94 Å/pix.
x 120 pix.
= 232.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.21108797 - 0.3168207
Average (Standard dev.)0.0030636673 (±0.020144612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 232.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_40049_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_40049_half_map_2.map
Annotationhalf map 2
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
    • Protein or peptide: Capsid protein

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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 / Macromolecule list: all / Details: Core protein Cp183 expressed in E coli
Source (natural)Organism: Hepatitis B virus

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 16.840186 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTAAALYRD ALESPEHCSP HHTALRQAIL CWGDLMTLAT WVGTNLEDPA SRDLVVSYV NTNVGLKFRQ LLWFHISCLT FGRETVLEYL VSFGVWIRTP PAYRPPNAPI LSTLPETAAA AA

UniProtKB: Capsid protein

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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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm
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.
Final reconstructionApplied 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 assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - 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)

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Atomic model buiding 1

DetailsA hexamer model was flexibly fitted into the hexamer maps using Alphafold, ISOLDE, PHENIX, and Coot.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8ghs:
Empty HBV Cp183 capsid with importin-beta, subparticle reconstruction at 2-fold location

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