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- PDB-7od6: Hepatitis B core protein + GSLLGRMKGA -

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Basic information

Entry
Database: PDB / ID: 7od6
TitleHepatitis B core protein + GSLLGRMKGA
Components
  • Capsid protein
  • Inhibitory Peptide P2 (GSLLGRMKGA)
KeywordsVIRUS LIKE PARTICLE / Hepatitis B core protein / inhibitory peptide
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
Biological speciesHepatitis B virus genotype D subtype ayw
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsBottcher, B. / Makbul, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)bo1150/17-1 Germany
CitationJournal: Microorganisms / Year: 2021
Title: Conformational Plasticity of Hepatitis B Core Protein Spikes Promotes Peptide Binding Independent of the Secretion Phenotype.
Authors: Cihan Makbul / Vladimir Khayenko / Hans Michael Maric / Bettina Böttcher /
Abstract: Hepatitis B virus is a major human pathogen, which forms enveloped virus particles. During viral maturation, membrane-bound hepatitis B surface proteins package hepatitis B core protein capsids. This ...Hepatitis B virus is a major human pathogen, which forms enveloped virus particles. During viral maturation, membrane-bound hepatitis B surface proteins package hepatitis B core protein capsids. This process is intercepted by certain peptides with an "LLGRMKG" motif that binds to the capsids at the tips of dimeric spikes. With microcalorimetry, electron cryo microscopy and peptide microarray-based screens, we have characterized the structural and thermodynamic properties of peptide binding to hepatitis B core protein capsids with different secretion phenotypes. The peptide "GSLLGRMKGA" binds weakly to hepatitis B core protein capsids and mutant capsids with a premature (F97L) or low-secretion phenotype (L60V and P5T). With electron cryo microscopy, we provide novel structures for L60V and P5T and demonstrate that binding occurs at the tips of the spikes at the dimer interface, splaying the helices apart independent of the secretion phenotype. Peptide array screening identifies "SLLGRM" as the core binding motif. This shortened motif binds only to one of the two spikes in the asymmetric unit of the capsid and induces a much smaller conformational change. Altogether, these comprehensive studies suggest that the tips of the spikes act as an autonomous binding platform that is unaffected by mutations that affect secretion phenotypes.
History
DepositionApr 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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  • Biological unit as author_defined_assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-12820
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  • Superimposition on EM map
  • EMDB-12820
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Structure viewerMolecule:
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Assembly

Deposited unit
B: Capsid protein
A: Capsid protein
C: Capsid protein
D: Capsid protein
F: Inhibitory Peptide P2 (GSLLGRMKGA)
E: Inhibitory Peptide P2 (GSLLGRMKGA)


Theoretical massNumber of molelcules
Total (without water)87,5896
Polymers87,5896
Non-polymers00
Water00
1
B: Capsid protein
A: Capsid protein
C: Capsid protein
D: Capsid protein
F: Inhibitory Peptide P2 (GSLLGRMKGA)
E: Inhibitory Peptide P2 (GSLLGRMKGA)
x 60


Theoretical massNumber of molelcules
Total (without water)5,255,313360
Polymers5,255,313360
Non-polymers00
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
Source: (gene. exp.) Hepatitis B virus genotype D subtype ayw (isolate France/Tiollais/1979)
Strain: isolate France/Tiollais/1979 / Production host: Escherichia coli (E. coli) / References: UniProt: P03146
#2: Protein/peptide Inhibitory Peptide P2 (GSLLGRMKGA)


Mass: 1501.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 4.8 MDa / Experimental value: NO
Source (natural)Organism: Hepatitis B virus / Strain: genotype D subtype ayw
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 360 nm / Triangulation number (T number): 4
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / 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: TFS 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: 800 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: 3.3 sec. / Electron dose: 52 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1578

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2RELION3.1particle selectiontemplate
3EPUimage acquisition
5CTFFIND4CTF correction
8PHENIXmodel fitting
9UCSF Chimeramodel fitting
10Cootmodel fitting
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
15RELION3.13D reconstruction
16PHENIXmodel refinement
17Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 110918
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66884 / Symmetry type: POINT
Atomic model buildingB value: 141 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 6HTX / Initial refinement model-ID: 1 / PDB-ID: 6HTX

6htx

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1c
2A
3B
4D
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069517
ELECTRON MICROSCOPYf_angle_d0.6817219
ELECTRON MICROSCOPYf_dihedral_angle_d6.7334129
ELECTRON MICROSCOPYf_chiral_restr0.072756
ELECTRON MICROSCOPYf_plane_restr0.0041386

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