+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10800 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Duck hepatitis B virus capsid | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Keywords | duck hepatitis B core protein / extension domain / spike / slowly folding / VIRUS LIKE PARTICLE | ||||||||||||
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 | ||||||||||||
Biological species | Hepatitis B virus duck/DHBV-16 | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Makbul C / Bottcher B | ||||||||||||
Funding support | Germany, 3 items
| ||||||||||||
Citation | Journal: Elife / Year: 2020 Title: Slowly folding surface extension in the prototypic avian hepatitis B virus capsid governs stability. Authors: Cihan Makbul / Michael Nassal / Bettina Böttcher / Abstract: Hepatitis B virus (HBV) is an important but difficult to study human pathogen. Most basics of the hepadnaviral life-cycle were unraveled using duck HBV (DHBV) as a model although DHBV has a capsid ...Hepatitis B virus (HBV) is an important but difficult to study human pathogen. Most basics of the hepadnaviral life-cycle were unraveled using duck HBV (DHBV) as a model although DHBV has a capsid protein (CP) comprising ~260 rather than ~180 amino acids. Here we present high-resolution structures of several DHBV capsid-like particles (CLPs) determined by electron cryo-microscopy. As for HBV, DHBV CLPs consist of a dimeric α-helical frame-work with protruding spikes at the dimer interface. A fundamental new feature is a ~ 45 amino acid proline-rich extension in each monomer replacing the tip of the spikes in HBV CP. In vitro, folding of the extension takes months, implying a catalyzed process in vivo. DHBc variants lacking a folding-proficient extension produced regular CLPs in bacteria but failed to form stable nucleocapsids in hepatoma cells. We propose that the extension domain acts as a conformational switch with differential response options during viral infection. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10800.map.gz | 226.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-10800-v30.xml emd-10800.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10800_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10800.png | 364 KB | ||
Masks | emd_10800_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-10800.cif.gz | 6.4 KB | ||
Others | emd_10800_half_map_1.map.gz emd_10800_half_map_2.map.gz | 222.9 MB 222.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10800 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10800 | HTTPS FTP |
-Validation report
Summary document | emd_10800_validation.pdf.gz | 439 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_10800_full_validation.pdf.gz | 438.1 KB | Display | |
Data in XML | emd_10800_validation.xml.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10800 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10800 | HTTPS FTP |
-Related structure data
Related structure data | 6yghMC 6ygiC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_10800.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_10800_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_10800_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_10800_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Hepatitis B virus duck/DHBV-16
Entire | Name: Hepatitis B virus duck/DHBV-16 |
---|---|
Components |
|
-Supramolecule #1: Hepatitis B virus duck/DHBV-16
Supramolecule | Name: Hepatitis B virus duck/DHBV-16 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 489543 / Sci species name: Hepatitis B virus duck/DHBV-16 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: Anas platyrhynchos (mallard) |
Molecular weight | Theoretical: 7.2 MDa |
Virus shell | Shell ID: 1 / Name: duck Hepatitis B virus capsid / Diameter: 370.0 Å / T number (triangulation number): 4 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Hepatitis B virus duck/DHBV-16 |
Molecular weight | Theoretical: 30.33851 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MDINASRALA NVYDLPDDFF PKIDDLVRDA KDALEPYWKS DSIKKHVLIA THFVDLIEDF WQTTQGMHEI AESLRAVIPP TTTPVPPGY LIQHEEAEEI PLGDLFKHQE ERIVSFQPDY PITARIHAHL KAYAKINEES LDRARRLLWW HYNCLLWGEA Q VTNYISRL ...String: MDINASRALA NVYDLPDDFF PKIDDLVRDA KDALEPYWKS DSIKKHVLIA THFVDLIEDF WQTTQGMHEI AESLRAVIPP TTTPVPPGY LIQHEEAEEI PLGDLFKHQE ERIVSFQPDY PITARIHAHL KAYAKINEES LDRARRLLWW HYNCLLWGEA Q VTNYISRL RTWLSTPEKY RGRDAPTIEA ITRPIQVAQG GRKTTTGTRK PRGLEPRRRK VKTTVVYGRR RSKSRERRAP TP QRAGSPL PRSSSSHHRS PSPRK UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.2 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| ||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.029 kPa | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: For the vitrification, grids (400 mesh copper grids (type R 1.2/1.3. Quantifoil Micro Tools, Jena/Germany) were rendered hydrophilic by glow discharging in air at a pressure of 29 Pa for 2 ...Details: For the vitrification, grids (400 mesh copper grids (type R 1.2/1.3. Quantifoil Micro Tools, Jena/Germany) were rendered hydrophilic by glow discharging in air at a pressure of 29 Pa for 2 minutes at medium power with a Plasma Cleaner (model PDC-002. Harrick Plasma Ithaca, NY/USA). Then, 3.5 ul of DHBc solution was pipetted onto the grids and they were plunge frozen in liquid ethane with a Vitrobot mark IV (FEI-Thermo Fisher Scientific). The settings for the Vitrobot were 3s blot time, 45 s wait time, blot force 0 at a temperature of 4 C and 100 % humidity. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2473 / Average exposure time: 75.0 sec. / Average electron dose: 77.0 e/Å2 Details: movie mode, 3 images per hole, 47 fractions per movie |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.1 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | PDB-6ygh: |