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- PDB-8bdz: Hepatitis B virus core antigen (HBc) with the insertion of four e... -

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Basic information

Entry
Database: PDB / ID: 8bdz
TitleHepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) with T=4 topology
ComponentsCore protein,Matrix protein 2,External core antigen
KeywordsVIRUS LIKE PARTICLE / HBc / M2e / VLP
Function / homology
Function and homology information


suppression by virus of host autophagy / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / protein complex oligomerization / proton transmembrane transporter activity / 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 ...suppression by virus of host autophagy / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / protein complex oligomerization / proton transmembrane transporter activity / 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 / virus-mediated perturbation of host defense response / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / RNA binding / extracellular region / membrane
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Influenza virus matrix protein 2 / Influenza Matrix protein (M2) / 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 adw/991
Influenza A virus
Hepatitis B virus genotype D subtype ayw
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsEgorov, V.V. / Shvetsov, A.V. / Pichkur, E.B. / Shaldzhyan, A.A. / Zabrodskaya, Y.A. / Vinogradova, D.S. / Nekrasov, P.A. / Gorshkov, A.N. / Garmay, Y.P. / Kovaleva, A.A. ...Egorov, V.V. / Shvetsov, A.V. / Pichkur, E.B. / Shaldzhyan, A.A. / Zabrodskaya, Y.A. / Vinogradova, D.S. / Nekrasov, P.A. / Gorshkov, A.N. / Garmay, Y.P. / Kovaleva, A.A. / Stepanova, L.A. / Tsybalova, L.M. / Shtam, T.A. / Myasnikov, A.G. / Konevega, A.L.
Funding support Russian Federation, 1items
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 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Core protein,Matrix protein 2,External core antigen
B: Core protein,Matrix protein 2,External core antigen
C: Core protein,Matrix protein 2,External core antigen


Theoretical massNumber of molelcules
Total (without water)92,5823
Polymers92,5823
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Core protein,Matrix protein 2,External core antigen / Proton channel protein M2 / HBeAg / Precore protein / p25


Mass: 30860.533 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus adw/991, (gene. exp.) Influenza A virus (A/Malaya/302/1954(H1N1)), (gene. exp.) Hepatitis B virus genotype D subtype ayw (isolate France/Tiollais/1979)
Gene: prec/C, M, M2 / Strain: A/Malaysia:Malaya/302/1954 H1N1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9E0P3, UniProt: A4K144, UniProt: P0C573

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (T=4)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 30.84 kDa/nm / Experimental value: NO
Source (natural)Organism: Hepatitis B virus
Source (recombinant)Organism: Escherichia col
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 0.05 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
1Warpparticle selection
2EPU1.9image acquisition
4WarpCTF correction
10RELIONinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 63404
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13146 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 68.95 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223411
ELECTRON MICROSCOPYf_angle_d0.49254662
ELECTRON MICROSCOPYf_chiral_restr0.0368525
ELECTRON MICROSCOPYf_plane_restr0.0041585
ELECTRON MICROSCOPYf_dihedral_angle_d3.8905447

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