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Yorodumi- EMDB-2278: cryoEM structure of hepatitis B virus core assembled from full-le... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2278 | |||||||||
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Title | cryoEM structure of hepatitis B virus core assembled from full-length core protein | |||||||||
Map data | Reconstruction of HBV | |||||||||
Sample |
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Keywords | hepatitis B virus core antigen (HBc) / HBV capsid maturation and envelopment | |||||||||
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 / virus-mediated perturbation of host defense response / structural molecule activity / DNA binding / RNA binding / extracellular region Similarity search - Function | |||||||||
Biological species | Hepatitis B virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Yu X / Jin L / Jih J / Shih C / Zhou ZH | |||||||||
Citation | Journal: PLoS One / Year: 2013 Title: 3.5Å cryoEM structure of hepatitis B virus core assembled from full-length core protein. Authors: Xuekui Yu / Lei Jin / Jonathan Jih / Chiaho Shih / Z Hong Zhou / Abstract: The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was ...The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM) and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149). Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90°) from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD) and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD's accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2278.map.gz | 180.1 MB | EMDB map data format | |
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Header (meta data) | emd-2278-v30.xml emd-2278.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | EMD-2278-HBV.jpg | 134.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2278 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2278 | HTTPS FTP |
-Validation report
Summary document | emd_2278_validation.pdf.gz | 454.8 KB | Display | EMDB validaton report |
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Full document | emd_2278_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | emd_2278_validation.xml.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2278 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2278 | HTTPS FTP |
-Related structure data
Related structure data | 3j2vMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2278.map.gz / Format: CCP4 / Size: 317.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of HBV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.9333 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Hepatitis B virus core assembled from full-length core protein
Entire | Name: Hepatitis B virus core assembled from full-length core protein |
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Components |
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-Supramolecule #1000: Hepatitis B virus core assembled from full-length core protein
Supramolecule | Name: Hepatitis B virus core assembled from full-length core protein type: sample / ID: 1000 / Oligomeric state: Icosahedral particle / Number unique components: 1 |
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Molecular weight | Experimental: 5 MDa / Theoretical: 5 MDa / Method: Based on amino acid sequences |
-Supramolecule #1: Hepatitis B virus
Supramolecule | Name: Hepatitis B virus / type: virus / ID: 1 / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Host system | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET-11a |
Molecular weight | Experimental: 5 MDa / Theoretical: 5 MDa |
Virus shell | Shell ID: 1 / Diameter: 360 Å / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jan 1, 2009 |
Image recording | Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.75 mm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMIRS / Number images used: 8093 |