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Yorodumi- EMDB-3268: Importin-beta can bind Hepatitis B Virus core protein and empty c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3268 | |||||||||
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Title | Importin-beta can bind Hepatitis B Virus core protein and empty core-like particles and induce structural changes | |||||||||
Map data | Cryo-EM reconstruction of unphosphorylated Cp183 and Imp-beta in NaCl | |||||||||
Sample |
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Keywords | HBV / Cp183 / Importin-beta | |||||||||
Biological species | Homo sapiens (human) / Hepatitis B virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.2 Å | |||||||||
Authors | Chen C / Wang JC-Y / Pierson EE / Kiefer DZ / Delaleau M / Gallucci L / Cazenave C / Kann M / Jarrold MF / Zlotnick A | |||||||||
Citation | Journal: PLoS Pathog / Year: 2016 Title: Importin β Can Bind Hepatitis B Virus Core Protein and Empty Core-Like Particles and Induce Structural Changes. Authors: Chao Chen / Joseph Che-Yen Wang / Elizabeth E Pierson / David Z Keifer / Mildred Delaleau / Lara Gallucci / Christian Cazenave / Michael Kann / Martin F Jarrold / Adam Zlotnick / Abstract: Hepatitis B virus (HBV) capsids are found in many forms: immature single-stranded RNA-filled cores, single-stranded DNA-filled replication intermediates, mature cores with relaxed circular double- ...Hepatitis B virus (HBV) capsids are found in many forms: immature single-stranded RNA-filled cores, single-stranded DNA-filled replication intermediates, mature cores with relaxed circular double-stranded DNA, and empty capsids. A capsid, the protein shell of the core, is a complex of 240 copies of core protein. Mature cores are transported to the nucleus by a complex that includes both importin α and importin β (Impα and Impβ), which bind to the core protein's C-terminal domains (CTDs). Here we have investigated the interactions of HBV core protein with importins in vitro. Strikingly, empty capsids and free core protein can bind Impβ without Impα. Cryo-EM image reconstructions show that the CTDs, which are located inside the capsid, can extrude through the capsid to be bound by Impβ. Impβ density localized on the capsid exterior near the quasi-sixfold vertices, suggested a maximum of 30 Impβ per capsid. However, examination of complexes using single molecule charge-detection mass spectrometry indicate that some complexes include over 90 Impβ molecules. Cryo-EM of capsids incubated with excess Impβ shows a population of damaged particles and a population of "dark" particles with internal density, suggesting that Impβ is effectively swallowed by the capsids, which implies that the capsids transiently open and close and can be destabilized by Impβ. Though the in vitro complexes with great excess of Impβ are not biological, these results have implications for trafficking of empty capsids and free core protein; activities that affect the basis of chronic HBV infection. | |||||||||
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_3268.map.gz | 61 MB | EMDB map data format | |
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Header (meta data) | emd-3268-v30.xml emd-3268.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_3268.png | 190.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3268 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3268 | HTTPS FTP |
-Validation report
Summary document | emd_3268_validation.pdf.gz | 211.3 KB | Display | EMDB validaton report |
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Full document | emd_3268_full_validation.pdf.gz | 210.4 KB | Display | |
Data in XML | emd_3268_validation.xml.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3268 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3268 | HTTPS FTP |
-Related structure data
Related structure data | 3266C 3267C 3269C 3270C 3271C 3272C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3268.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of unphosphorylated Cp183 and Imp-beta in NaCl | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.512 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 : 7.9 uM Cp183 dimer in capsid form and 5.3 uM Imp-beta in NaCl
Entire | Name: 7.9 uM Cp183 dimer in capsid form and 5.3 uM Imp-beta in NaCl |
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Components |
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-Supramolecule #1000: 7.9 uM Cp183 dimer in capsid form and 5.3 uM Imp-beta in NaCl
Supramolecule | Name: 7.9 uM Cp183 dimer in capsid form and 5.3 uM Imp-beta in NaCl type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: Hepatitis B virus
Supramolecule | Name: Hepatitis B virus / type: virus / ID: 1 / Name.synonym: HBV / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Sci species strain: adyw / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: HBV |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Host system | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 (DE3) cells / Recombinant plasmid: pET11cCp183 |
Molecular weight | Experimental: 4.8 MDa / Theoretical: 4.8 MDa |
Virus shell | Shell ID: 1 / Name: Cp183 / T number (triangulation number): 4 |
-Macromolecule #1: importin beta
Macromolecule | Name: importin beta / type: protein_or_peptide / ID: 1 / Name.synonym: Imp-beta / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: PET30a |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.28 mg/mL |
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Buffer | pH: 7.4 / Details: 0.15M NaCl, 10 mM DTT, 20 mM Tris-HCl |
Grid | Details: glow-discharged holey carbon grid (Quantifoil R2/2) or continuous carbon film coated grid (EMS) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 98 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 4 seconds before plunging |
-Electron microscopy
Microscope | JEOL 3200FS |
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Temperature | Average: 98 K |
Specialist optics | Energy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | Weak beam illumination |
Date | Nov 17, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 159 / 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: 1.1 mm / Nominal defocus max: 4.04 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | Data processed by auto3dem |
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CTF correction | Details: each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: OTHER / Software - Name: Auto3dem / Number images used: 12776 |