+Open data
-Basic information
Entry | Database: PDB / ID: 8px6 | ||||||||||||||||||
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Title | Hepatitis B core protein with bound SLLGRM-dimer | ||||||||||||||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Hepatitis B core protein / Spikes SLLGRM-dimer aggregator Hepatitis B virus Capsid LIKE PARTICLE | ||||||||||||||||||
Function / homology | Hepatitis 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 species | Hepatitis B virus synthetic construct (others) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||||||||
Authors | Makbul, C. / Khayenko, V. / Maric, M.H. / Bottcher, B. | ||||||||||||||||||
Funding support | Germany, 5items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8px6.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8px6.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 8px6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8px6_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8px6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8px6_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 8px6_validation.cif.gz | 54.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/8px6 ftp://data.pdbj.org/pub/pdb/validation_reports/px/8px6 | HTTPS FTP |
-Related structure data
Related structure data | 18001MC 8pwoC 8px3C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hepatitis B virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 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 virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Homo sapiens |
Virus shell | Diameter: 360 nm / Triangulation number (T number): 4 |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 320845 / Details: template picked | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132610 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7OD4 Accession code: 7OD4 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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