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- EMDB-22135: HBV holey capsid missing 18 dimers -

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Basic information

Entry
Database: EMDB / ID: EMD-22135
TitleHBV holey capsid missing 18 dimers
Map data
Sample
  • Complex: HBV holey capsid produced by disassemlby
    • Other: HBV Cp150 dimer
Biological speciesHepatitis B virus subtype adyw
Methodsingle particle reconstruction / cryo EM / Resolution: 12.9 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: 0.0112
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0112
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22135.png

Downloads & links

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Map

FileDownload / File: emd_22135.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.51 Å/pix.
x 120 pix.
= 541.44 Å		4.51 Å/pix.
x 120 pix.
= 541.44 Å		4.51 Å/pix.
x 120 pix.
= 541.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0112 / Movie #1: 0.0112
Minimum - Maximum-0.0652352 - 0.121770926
Average (Standard dev.)5.5557895e-05 (±0.00813553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 541.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.5124.5124.512
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z541.440541.440541.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.0650.1220.000

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Supplemental data

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Sample components

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Entire : HBV holey capsid produced by disassemlby

EntireName: HBV holey capsid produced by disassemlby
Components
  • Complex: HBV holey capsid produced by disassemlby
    • Other: HBV Cp150 dimer

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Supramolecule #1: HBV holey capsid produced by disassemlby

SupramoleculeName: HBV holey capsid produced by disassemlby / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus subtype adyw
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: HBV Cp150 dimer

MacromoleculeName: HBV Cp150 dimer / type: other / ID: 1 / Classification: other
Source (natural)Organism: Hepatitis B virus subtype adyw
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTAAALYRD ALESPEHASP HHTALRQAIL AWGDLMTLAT WVGTNLEDPA SRDLVVSYVN TNVGLKFRQL LWFHISALTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7882
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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