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- PDB-8px3: Hepatitis B core protein with bound P1dC -

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Basic information

Entry
Database: PDB / ID: 8px3
TitleHepatitis B core protein with bound P1dC
Components
  • External core antigen
  • P1dC
KeywordsVIRUS LIKE PARTICLE / Hepatitis B core protein / Spikes dimeric peptide binder aggregator Hepatitis B virus Capsid LIKE PARTICLE
Function / homologyHepatitis 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 / structural molecule activity / extracellular region / External core antigen
Function and homology information
Biological speciesHepatitis B virus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMakbul, C. / Khayenko, V. / Maric, M.H. / Bottcher, B.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)BO1150/17-1 Germany
German Research Foundation (DFG)MA6957/1-1 Germany
German Research Foundation (DFG)INST 93/903-1 Germany
German Research Foundation (DFG)INST 93/1042-1 Germany
German Research Foundation (DFG)INST 93/1143-1 Germany
CitationJournal: Elife / Year: 2025
Title: Induction of hepatitis B core protein aggregation targeting an unconventional binding site
Authors: Khayenko, V. / Makbul, C. / Schulte, C. / Hemmelmann, N. / Kachler, S. / Bottcher, B. / Maric, H.M. / Comas-Garcia, M. / Dotsch, V.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: External core antigen
A: External core antigen
C: External core antigen
D: External core antigen
F: P1dC
E: P1dC


Theoretical massNumber of molelcules
Total (without water)86,6636
Polymers86,6636
Non-polymers00
Water00
1
B: External core antigen
A: External core antigen
C: External core antigen
D: External core antigen
F: P1dC
E: P1dC
x 60


Theoretical massNumber of molelcules
Total (without water)5,199,805360
Polymers5,199,805360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
External core antigen


Mass: 21146.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Production host: Escherichia coli (E. coli) / References: UniProt: W6CP35
#2: Protein/peptide P1dC


Mass: 1039.273 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The binder consists of 2 peptide moieties linked by a PEG-linker: The peptide moiety is 'MHRSLLGRMKGA' The resolved density has a length of 6 residues of the moiety. The position is ...Details: The binder consists of 2 peptide moieties linked by a PEG-linker: The peptide moiety is 'MHRSLLGRMKGA' The resolved density has a length of 6 residues of the moiety. The position is unresolved and modelled as Poly-Ala
Source: (synth.) synthetic construct (others)
Has protein modificationN

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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 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Hepatitis B virus / Strain: ayw/France/Tiollais/1979
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 360 nm / Triangulation number (T number): 4
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2784
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3.1particle selection
3EPUimage acquisition
5CTFFIND4CTF correction
8UCSF Chimeramodel fitting
9PHENIXmodel fitting
10Cootmodel fitting
14RELION3.1initial Euler assignment
16cryoSPARC4final Euler assignment
19cryoSPARC43D reconstructionnone uniform refinement
21PHENIXmodel refinement
22Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 36817 / Details: template picked
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22830 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7OD4

7od4


Accession code: 7OD4 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0054871
ELECTRON MICROSCOPYf_angle_d0.5856672
ELECTRON MICROSCOPYf_dihedral_angle_d5.7793414
ELECTRON MICROSCOPYf_chiral_restr0.04759
ELECTRON MICROSCOPYf_plane_restr0.004846

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