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 8BDZ | pdb_00008bdz

Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) with T=4 topology


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8BDZ

This is version 1.1 of the entry. See complete history. 

Literature

Inside and outside of virus-like particles HBc and HBc/4M2e: A comprehensive study of the structure.

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.

(2022) Biophys Chem 293: 106943-106943

  • DOI: https://doi.org/10.1016/j.bpc.2022.106943
  • Primary Citation Related Structures: 
    8BDZ, 8BER

  • PubMed 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 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.


  • Organizational Affiliation: 
    • Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation; Institute of Experimental Medicine, Academika Pavlova, 12, 197376 St. Petersburg, Russian Federation. Electronic address: sondyn@yandex.ru.

Macromolecule Content 

  • Total Structure Weight: 92.58 kDa 
  • Atom Count: 3,309 
  • Modeled Residue Count: 414 
  • Deposited Residue Count: 867 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Core protein,Matrix protein 2,External core antigen
A, B, C
289Hepatitis B virus adw/991, Influenza A virus (A/Malaya/302/1954(H1N1)), Hepatitis B virus ayw/France/Tiollais/1979Mutation(s): 0 
Gene Names: prec/C, M, M2
UniProt
Find proteins for A4K144 (Influenza A virus (strain A/Malaysia:Malaya/302/1954 H1N1))
Explore A4K144 
Go to UniProtKB:  A4K144
Find proteins for P0C573 (Hepatitis B virus genotype D subtype ayw (isolate France/Tiollais/1979))
Explore P0C573 
Go to UniProtKB:  P0C573
Find proteins for Q9E0P3 (Hepatitis B virus)
Explore Q9E0P3 
Go to UniProtKB:  Q9E0P3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0C573A4K144Q9E0P3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation19-74-20146

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary