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- EMDB-37631: Hepatitis B virus capsid (HBV core protein) -

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Basic information

Entry
Database: EMDB / ID: EMD-37631
TitleHepatitis B virus capsid (HBV core protein)
Map data
Sample
  • Complex: Hepatitis B virus capsid
    • Protein or peptide: Hepatitis B virus core protein
KeywordsViral core capsid / Icosahedral / SPLICING
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsYip RPH / Lai LTF / Lau WCY / Ngo JCK / Kwok DCY
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14177317 Hong Kong
CitationJournal: PLoS Pathog / Year: 2024
Title: SRPK2 Mediates HBV Core Protein Phosphorylation and Capsid Assembly via Docking Interaction.
Authors: Ryan Pak Hong Yip / Doris Ching Ying Kwok / Louis Tung Faat Lai / Siu-Ming Ho / Ivan Chun Kit Wong / Chi-Ping Chan / Wilson Chun Yu Lau / Jacky Chi Ki Ngo /
Abstract: Members of the serine-arginine protein kinase (SRPK) family, SRPK1 and SRPK2, phosphorylate the hepatitis B core protein (Cp) and are crucial for pregenomic RNA encapsidation during viral ...Members of the serine-arginine protein kinase (SRPK) family, SRPK1 and SRPK2, phosphorylate the hepatitis B core protein (Cp) and are crucial for pregenomic RNA encapsidation during viral nucleocapsid assembly. Among them, SRPK2 exhibits higher kinase activity toward Cp. In this study, we identified Cp sites that are phosphorylated by SRPK2 and demonstrated that the kinase utilizes an SRPK-specific docking groove to interact with and regulate the phosphorylation of the C-terminal arginine rich domain of Cp. We determined that direct interaction between the docking groove of SRPK2 and unphosphorylated Cp inhibited premature viral capsid assembly in vitro, whereas the phosphorylation of the viral protein reactivated the process. Pull-down assays together with the new cryo-electron microscopy structure of the HBV capsid in complex with SRPK2 revealed that the kinases decorate the surface of the viral capsid by interacting with the C-terminal domain of Cp, underscoring the importance of the docking interaction in regulating capsid assembly and pregenome packaging. Moreover, SRPK2-knockout in HepG2 cells suppressed Cp phosphorylation, indicating that SRPK2 is an important cellular kinase for HBV life cycle.
History
DepositionOct 1, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37631.png

Downloads & links

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Map

FileDownload / File: emd_37631.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.938 Å
Density
Contour LevelBy AUTHOR: 0.0232
Minimum - Maximum-0.046052847 - 0.12116444
Average (Standard dev.)0.0013797791 (±0.010925388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 465.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37631_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37631_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37631_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Hepatitis B virus capsid

EntireName: Hepatitis B virus capsid
Components
  • Complex: Hepatitis B virus capsid
    • Protein or peptide: Hepatitis B virus core protein

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Supramolecule #1: Hepatitis B virus capsid

SupramoleculeName: Hepatitis B virus capsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 5.64 MDa

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Macromolecule #1: Hepatitis B virus core protein

MacromoleculeName: Hepatitis B virus core protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGNNLEDPA SRDLVVNYVN TNMGLKIRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR ...String:
MGSSHHHHHH SSGLVPRGSH MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGNNLEDPA SRDLVVNYVN TNMGLKIRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR RRDRGRSPRR RTPSPRRRRS QSPRRRRSQS RESQC

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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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS F200C
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 270 / Average exposure time: 54.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6042
Startup modelType of model: EMDB MAP
EMDB ID:

3015

Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1.2)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 1773
FSC plot (resolution estimation)

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