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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12821 | |||||||||
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Title | Hepatitis B core protein + SLLGRM | |||||||||
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![]() | Hepatitis B core protein / VIRUS LIKE PARTICLE / inhibitory peptide | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Bottcher B / Makbul C | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 228 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.5 KB | Display | ![]() |
Images | ![]() | 221.1 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 256.9 MB 256.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7od7MC ![]() 7ocoC ![]() 7ocwC ![]() 7od4C ![]() 7od6C ![]() 7od8C ![]() 7oenC ![]() 7oevC ![]() 7oewC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_12821_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12821_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Hepatitis B virus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Hepatitis B virus
Supramolecule | Name: Hepatitis B virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Sci species strain: genotype D subtype ayw / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.8 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 360.0 Å / T number (triangulation number): 4 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: isolate France/Tiollais/1979 |
Molecular weight | Theoretical: 21.146217 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYV NTNMGLKFRQ LLWFHISCLT FGRETVIEYL VSFGVWIRTP PAYRPPNAPI LSTLPETTVV RRRGRSPRRR T PSPRRRRS QSPRRRRSQS RESQC UniProtKB: Capsid protein |
-Macromolecule #2: SLLRGM
Macromolecule | Name: SLLRGM / type: protein_or_peptide / ID: 2 / Details: SLLRGM / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.187479 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)SLLR GM |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2547 / Average exposure time: 2.4 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 119 | ||||||||||
Output model | ![]() PDB-7od7: |