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- EMDB-29858: Hepatitis B virus capsid bound to importin alpha1 -

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Basic information

Entry
Database: EMDB / ID: EMD-29858
TitleHepatitis B virus capsid bound to importin alpha1
Map data
Sample
  • Complex: Capsid formed by Cp183 when importin alpha1 is incorporated
    • Protein or peptide: Core protein Cp183
KeywordsCapsid formed by Cp183 when bound to importin alpha1 / VIRUS LIKE PARTICLE
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 / extracellular region
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / 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: 3.8 Å
AuthorsYang R / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2024
Title: Structural basis for nuclear import of hepatitis B virus (HBV) nucleocapsid core.
Authors: Ruoyu Yang / Ying-Hui Ko / Fenglin Li / Ravi K Lokareddy / Chun-Feng David Hou / Christine Kim / Shelby Klein / Santiago Antolínez / Juan F Marín / Carolina Pérez-Segura / Martin F ...Authors: Ruoyu Yang / Ying-Hui Ko / Fenglin Li / Ravi K Lokareddy / Chun-Feng David Hou / Christine Kim / Shelby Klein / Santiago Antolínez / Juan F Marín / Carolina Pérez-Segura / Martin F Jarrold / Adam Zlotnick / Jodi A Hadden-Perilla / Gino Cingolani /
Abstract: Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an ...Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an intact particle, hijacking human importins in a reaction stimulated by host kinases. This paper describes the mechanisms of HBV capsid recognition by importins. We found that importin α1 binds a nuclear localization signal (NLS) at the far end of the HBV coat protein Cp183 carboxyl-terminal domain (CTD). This NLS is exposed to the capsid surface through a pore at the icosahedral quasi-sixfold vertex. Phosphorylation at serine-155, serine-162, and serine-170 promotes CTD compaction but does not affect the affinity for importin α1. The binding of 30 importin α1/β1 augments HBV capsid diameter to ~620 angstroms, close to the maximum size trafficable through the NPC. We propose that phosphorylation favors CTD externalization and prompts its compaction at the capsid surface, exposing the NLS to importins.
History
DepositionFeb 20, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29858.png

Downloads & links

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Map

FileDownload / File: emd_29858.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 480 pix.
= 531.84 Å		1.11 Å/pix.
x 480 pix.
= 531.84 Å		1.11 Å/pix.
x 480 pix.
= 531.84 Å

Surface

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.108 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.03192083 - 0.084303856
Average (Standard dev.)0.00096620974 (±0.0043954765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 531.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29858_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29858_half_map_2.map
Projections & Slices
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Sample components

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Entire : Capsid formed by Cp183 when importin alpha1 is incorporated

EntireName: Capsid formed by Cp183 when importin alpha1 is incorporated
Components
  • Complex: Capsid formed by Cp183 when importin alpha1 is incorporated
    • Protein or peptide: Core protein Cp183

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Supramolecule #1: Capsid formed by Cp183 when importin alpha1 is incorporated

SupramoleculeName: Capsid formed by Cp183 when importin alpha1 is incorporated
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus

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Macromolecule #1: Core protein Cp183

MacromoleculeName: Core protein Cp183 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 16.328719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYV NTNMGLKFRQ LLWFHISCLT FGRETVIEYL VSFGVWIRTP PAYRPPNAPI LSTLP

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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1qgt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37698
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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