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- EMDB-22133: HBV heterodimer hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-22133
TitleHBV heterodimer hexamer
Map data
Sample
  • Complex: Hexamer assembled from heterodimers
    • Other: HBV re-engineered capsid protein heterodimer
Biological speciesHepatitis B virus subtype adyw
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 17.0 Å
AuthorsZhao Z / Wang JC / Zlotnick A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01- AI144022 United States
CitationJournal: 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
DepositionJun 10, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0384
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0384
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22133.png

Downloads & links

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Map

FileDownload / File: emd_22133.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.6 Å
Density
Contour LevelBy AUTHOR: 0.0384 / Movie #1: 0.0384
Minimum - Maximum-0.0991069 - 0.2546032
Average (Standard dev.)7.084843e-05 (±0.009016458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.64.64.6
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
D min/max/mean-0.0990.2550.000

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Supplemental data

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Sample components

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Entire : Hexamer assembled from heterodimers

EntireName: Hexamer assembled from heterodimers
Components
  • Complex: Hexamer assembled from heterodimers
    • Other: HBV re-engineered capsid protein heterodimer

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Supramolecule #1: Hexamer assembled from heterodimers

SupramoleculeName: Hexamer assembled from heterodimers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus subtype adyw
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 205 KDa

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Macromolecule #1: HBV re-engineered capsid protein heterodimer

MacromoleculeName: HBV re-engineered capsid protein heterodimer / type: other / ID: 1 / Classification: other
Source (natural)Organism: Hepatitis B virus subtype adyw
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTAAALYRD ALESPEHCSP HHTALRQAIL CWGDLMTLAT WVGTNLEDPA SRDLVVSYVN TNVGLKFRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVH HHHHH
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Formate
GridDetails: unspecified
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeJEOL 1400
Image recordingFilm or detector model: OTHER / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

DetailsGatan Oneview 4k x 4k
Startup modelType of model: OTHER / Details: stochastic gradient descent
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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