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- PDB-8pwo: Hepatitis B core protein with bound Geraniol -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8pwo
TitleHepatitis B core protein with bound Geraniol
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / geraniol Hepatitis B core protein hyfrophobic pocket pocket factor Hepatitis B virus
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Geraniol / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus ayw/France/Tiollais/1979
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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 21, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Capsid protein
A: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2028
Polymers84,5854
Non-polymers6174
Water00
1
B: Capsid protein
A: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,112,112480
Polymers5,075,092240
Non-polymers37,020240
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Capsid protein / Core antigen / Core protein / HBcAg / p21.5


Mass: 21146.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: capsid has bound geraniol
Source: (gene. exp.) Hepatitis B virus ayw/France/Tiollais/1979
Production host: Escherichia coli (E. coli) / References: UniProt: P03146
#2: Chemical
ChemComp-64Z / Geraniol


Mass: 154.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: #1 / 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 supportDetails: plasma cleaner (model PDC-002. Harrick Plasma, Ithaca, NY, USA); at medium power of the instrument
Grid 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: 1200 nm / Nominal defocus min: 600 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: 3 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: 4875
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryFitting-ID
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting1
9RELION3.1initial Euler assignment
10RELION4final Euler assignment
12RELION43D reconstruction
13PHENIXmodel refinement1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 331635 / Details: template picked
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229646 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1RIGID BODY FITREAL
2
3
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069143
ELECTRON MICROSCOPYf_angle_d0.61816471
ELECTRON MICROSCOPYf_dihedral_angle_d6.3173743
ELECTRON MICROSCOPYf_chiral_restr0.041732
ELECTRON MICROSCOPYf_plane_restr0.0041362

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