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- PDB-8px6: Hepatitis B core protein with bound SLLGRM-dimer -

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Basic information

Entry
Database: PDB / ID: 8px6
TitleHepatitis B core protein with bound SLLGRM-dimer
Components
  • External core antigen
  • SLLGRM-dimer
KeywordsVIRUS LIKE PARTICLE / Hepatitis B core protein / Spikes SLLGRM-dimer 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 / virus-mediated perturbation of host defense response / 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: 2.5 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: To Be Published
Title: Peptide dimers aggregate Hepatitis B core proteins in live cells
Authors: Khayenko, V. / Makbul, C. / Schulte, C. / Hemmelmann, N. / Bottcher, B. / Maric, H.M.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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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
M: SLLGRM-dimer
E: SLLGRM-dimer


Theoretical massNumber of molelcules
Total (without water)85,9396
Polymers85,9396
Non-polymers00
Water00
1
B: External core antigen
A: External core antigen
C: External core antigen
D: External core antigen
M: SLLGRM-dimer
E: SLLGRM-dimer
x 60


Theoretical massNumber of molelcules
Total (without water)5,156,314360
Polymers5,156,314360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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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 SLLGRM-dimer


Mass: 676.850 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This is a synthetic peptide with two moieties of SLLGRM that are linked by a PEG linker The density that is assigned to SLLGRM is modelled as Poly-Ala.
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: 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: 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: 2.6 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: 4956
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
14PHENIXmodel refinement
15Cootmodel refinement
16RELION3.1initial Euler assignment
18cryoSPARC4final Euler assignment
21cryoSPARC43D reconstructionnone uniform refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 320845 / Details: template picked
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132610 / 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_d0.0089285
ELECTRON MICROSCOPYf_angle_d0.69416784
ELECTRON MICROSCOPYf_dihedral_angle_d7.0563764
ELECTRON MICROSCOPYf_chiral_restr0.047742
ELECTRON MICROSCOPYf_plane_restr0.0051356

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