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- EMDB-16009: Hepatitis B virus core antigen (HBc) with the insertion of four e... -

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Basic information

Entry
Database: EMDB / ID: EMD-16009
TitleHepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) with T=3 topology
Map data
Sample
  • Complex: Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (T=3)
    • Protein or peptide: Core protein,Matrix protein 2,External core antigen
KeywordsHBc / M2e / VLP / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated suppression of host autophagy / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / symbiont genome entry into host cell via pore formation in plasma membrane / viral penetration into host nucleus / host cell / host cell cytoplasm ...symbiont-mediated suppression of host autophagy / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / symbiont genome entry into host cell via pore formation in plasma membrane / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / extracellular region / membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2) / 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
Matrix protein 2 / External core antigen / Core protein
Similarity search - Component
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsEgorov VV / Shvetsov AV / Pichkur EB / Shaldzhyan AA / Zabrodskaya YA / Vinogradova DS / Nekrasov PA / Gorshkov AN / Garmay YP / Kovaleva AA ...Egorov VV / Shvetsov AV / Pichkur EB / Shaldzhyan AA / Zabrodskaya YA / Vinogradova DS / Nekrasov PA / Gorshkov AN / Garmay YP / Kovaleva AA / Stepanova LA / Tsybalova LM / Shtam TA / Myasnikov AG / Konevega AL
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20146 Russian Federation
CitationJournal: Biophys Chem / Year: 2023
Title: Inside and outside of virus-like particles HBc and HBc/4M2e: A comprehensive study of the structure.
Authors: V V Egorov / A V Shvetsov / E B Pichkur / A A Shaldzhyan / Ya A Zabrodskaya / D S Vinogradova / P A Nekrasov / A N Gorshkov / Yu P Garmay / A A Kovaleva / L A Stepanova / L M Tsybalova / T A ...Authors: V V Egorov / A V Shvetsov / E B Pichkur / A A Shaldzhyan / Ya A Zabrodskaya / D S Vinogradova / P A Nekrasov / A N Gorshkov / Yu P Garmay / A A Kovaleva / L A Stepanova / L M Tsybalova / T A Shtam / A G Myasnikov / A L Konevega /
Abstract: Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) form virus-like particles whose structure was studied using a combination of ...Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) form virus-like particles whose structure was studied using a combination of molecular modeling and cryo-electron microscopy (cryo-EM). It was also shown that self-assembling of the particles occurs inside bacterial cells, but despite the big inner volume of the core shell particle, purified HBc/4M2e contain an insignificant amount of bacterial proteins. It was shown that a fragment of the M2e corresponding to 4M2e insertion is prone to formation of amyloid-like fibrils. However, as the part of the immunodominant loop, M2e insertion does not show a tendency to intermolecular interaction. A full-atomic HBc-4M2e model with the resolution of about 3 Å (3.13 Å for particles of Т = 4 symmetry, 3.7 Å for particles of Т = 3 symmetry) was obtained by molecular modeling methods based on cryo-EM data.
History
DepositionOct 21, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16009.png

Downloads & links

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Map

FileDownload / File: emd_16009.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 440 pix.
= 487.08 Å		1.11 Å/pix.
x 440 pix.
= 487.08 Å		1.11 Å/pix.
x 440 pix.
= 487.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.107 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.75
Minimum - Maximum-0.70262945 - 3.417307
Average (Standard dev.)0.07946644 (±0.32824314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 487.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16009_msk_1.map
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Half map: #2

Fileemd_16009_half_map_1.map
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Half map: #1

Fileemd_16009_half_map_2.map
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Sample components

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Entire : Hepatitis B virus core antigen (HBc) with the insertion of four e...

EntireName: Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (T=3)
Components
  • Complex: Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (T=3)
    • Protein or peptide: Core protein,Matrix protein 2,External core antigen

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Supramolecule #1: Hepatitis B virus core antigen (HBc) with the insertion of four e...

SupramoleculeName: Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (T=3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 30.84 kDa/nm

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Macromolecule #1: Core protein,Matrix protein 2,External core antigen

MacromoleculeName: Core protein,Matrix protein 2,External core antigen / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus / Strain: isolate France/Tiollais/1979
Molecular weightTheoretical: 30.959662 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPYKEFGAT VELLSFLPSD FFPSVRDLLD TASALYREAL ESPEHCSPHH TALRQAILCW GELMTLATWV GGNLEDGSGT SGSSGSGSG GSGSGGGGEL SLLTEVETPI RNEWGSRSND SSDDLSLLTE VETPIRNEWG SRSNDSSDDL SLLTEVETPI R NEWGSRSN ...String:
MDPYKEFGAT VELLSFLPSD FFPSVRDLLD TASALYREAL ESPEHCSPHH TALRQAILCW GELMTLATWV GGNLEDGSGT SGSSGSGSG GSGSGGGGEL SLLTEVETPI RNEWGSRSND SSDDLSLLTE VETPIRNEWG SRSNDSSDDL SLLTEVETPI R NEWGSRSN DSSDDLSLLT EVETPIRNEW GSRSNDSSDD IGTSGSSGSG SGGSGSGGGG GPSRDLVVSY VNTNMGLKFR QL LWFHISC LTFGRETVIE YLVSFGVWIR TPPAYRPPNA PILSTLPETT VVC

UniProtKB: Core protein, Matrix protein 2, External core antigen

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00026000000000000003 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.05 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4757
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: cryoSPARC

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