+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29858 | |||||||||
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Title | Hepatitis B virus capsid bound to importin alpha1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Capsid formed by Cp183 when bound to importin alpha1 / 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 / 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: 3.8 Å | |||||||||
Authors | Yang R / Cingolani G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structural basis for nuclear import of hepatitis B virus (HBV) nucleocapsid core. Authors: Ruoyu Yang / Ying-Hui Ko / Fenglin Li / Ravi K Lokareddy / Chun-Feng David Hou / Christine Kim / Shelby Klein / Santiago Antolínez / Juan F Marín / Carolina Pérez-Segura / Martin F ...Authors: Ruoyu Yang / Ying-Hui Ko / Fenglin Li / Ravi K Lokareddy / Chun-Feng David Hou / Christine Kim / Shelby Klein / Santiago Antolínez / Juan F Marín / Carolina Pérez-Segura / Martin F Jarrold / Adam Zlotnick / Jodi A Hadden-Perilla / Gino Cingolani / Abstract: Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an ...Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an intact particle, hijacking human importins in a reaction stimulated by host kinases. This paper describes the mechanisms of HBV capsid recognition by importins. We found that importin α1 binds a nuclear localization signal (NLS) at the far end of the HBV coat protein Cp183 carboxyl-terminal domain (CTD). This NLS is exposed to the capsid surface through a pore at the icosahedral quasi-sixfold vertex. Phosphorylation at serine-155, serine-162, and serine-170 promotes CTD compaction but does not affect the affinity for importin α1. The binding of 30 importin α1/β1 augments HBV capsid diameter to ~620 angstroms, close to the maximum size trafficable through the NPC. We propose that phosphorylation favors CTD externalization and prompts its compaction at the capsid surface, exposing the NLS to importins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29858.map.gz | 394.8 MB | EMDB map data format | |
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Header (meta data) | emd-29858-v30.xml emd-29858.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29858_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_29858.png | 145.6 KB | ||
Filedesc metadata | emd-29858.cif.gz | 5.2 KB | ||
Others | emd_29858_half_map_1.map.gz emd_29858_half_map_2.map.gz | 385.5 MB 388.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29858 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29858 | HTTPS FTP |
-Validation report
Summary document | emd_29858_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29858_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29858_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | emd_29858_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29858 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29858 | HTTPS FTP |
-Related structure data
Related structure data | 8g8yMC 7umiC 8g5vC 8g6vC 8gcnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29858.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.108 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29858_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29858_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Capsid formed by Cp183 when importin alpha1 is incorporated
Entire | Name: Capsid formed by Cp183 when importin alpha1 is incorporated |
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Components |
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-Supramolecule #1: Capsid formed by Cp183 when importin alpha1 is incorporated
Supramolecule | Name: Capsid formed by Cp183 when importin alpha1 is incorporated type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Hepatitis B virus |
-Macromolecule #1: Core protein Cp183
Macromolecule | Name: Core protein Cp183 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Hepatitis B virus |
Molecular weight | Theoretical: 16.328719 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYV NTNMGLKFRQ LLWFHISCLT FGRETVIEYL VSFGVWIRTP PAYRPPNAPI LSTLP UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |