+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22133 | |||||||||
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Title | HBV heterodimer hexamer | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Hepatitis B virus subtype adyw | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 17.0 Å | |||||||||
Authors | Zhao Z / Wang JC / Zlotnick A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Asymmetrizing an icosahedral virus capsid by hierarchical assembly of subunits with designed asymmetry. Authors: Zhongchao Zhao / Joseph Che-Yen Wang / Mi Zhang / Nicholas A Lyktey / Martin F Jarrold / Stephen C Jacobson / Adam Zlotnick / Abstract: Symmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these ...Symmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these investigations. A means to create asymmetric capsids may expand applications. Here, starting with homodimeric Hepatitis B Virus capsid protein, we develop a heterodimer, design a hierarchical assembly pathway, and produce asymmetric capsids. In the heterodimer, the two halves have different growth potentials and assemble into hexamers. These preformed hexamers can nucleate co-assembly with other dimers, leading to Janus-like capsids with a small discrete hexamer patch. We can remove the patch specifically and observe asymmetric holey capsids by cryo-EM reconstruction. The resulting hole in the surface can be refilled with fluorescently labeled dimers to regenerate an intact capsid. In this study, we show how an asymmetric subunit can be used to generate an asymmetric particle, creating the potential for a capsid with different surface chemistries. | |||||||||
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_22133.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-22133-v30.xml emd-22133.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_22133.png | 46.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22133 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22133 | HTTPS FTP |
-Validation report
Summary document | emd_22133_validation.pdf.gz | 293.2 KB | Display | EMDB validaton report |
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Full document | emd_22133_full_validation.pdf.gz | 292.7 KB | Display | |
Data in XML | emd_22133_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22133 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22133 | HTTPS FTP |
-Related structure data
Related structure data | 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_22133.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 4.6 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 : Hexamer assembled from heterodimers
Entire | Name: Hexamer assembled from heterodimers |
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Components |
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-Supramolecule #1: Hexamer assembled from heterodimers
Supramolecule | Name: Hexamer assembled from heterodimers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Hepatitis B virus subtype adyw |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 205 KDa |
-Macromolecule #1: HBV re-engineered capsid protein heterodimer
Macromolecule | Name: HBV re-engineered capsid protein heterodimer / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Hepatitis B virus subtype adyw |
Sequence | String: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTAAALYRD ALESPEHCSP HHTALRQAIL CWGDLMTLAT WVGTNLEDPA SRDLVVSYVN TNVGLKFRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVH HHHHH |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
Grid | Details: unspecified |
Vitrification | Cryogen name: OTHER |
-Electron microscopy
Microscope | JEOL 1400 |
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Image recording | Film or detector model: OTHER / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |