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- EMDB-4651: Packaging of DNA Origami in Viral Capsids -

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Basic information

Entry
Database: EMDB / ID: EMD-4651
TitlePackaging of DNA Origami in Viral Capsids
Map dataSphere DNA origami encapsulated by SV40 VP1 capsid
Sample
  • Virus: Simian virus 40
Biological speciesSimian virus 40
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsKopatz I / Zalk R / Levi-Kalisman Y / Zlotkin-Rivkin E / Frank GA / Kler S
CitationJournal: Nanoscale / Year: 2019
Title: Packaging of DNA origami in viral capsids.
Authors: Idit Kopatz / Ran Zalk / Yael Levi-Kalisman / Efrat Zlotkin-Rivkin / Gabriel A Frank / Stanislav Kler /
Abstract: Here we show the encapsulation of 35 nm diameter, nearly-spherical, DNA origami by self-assembly of SV40-like (simian virus 40) particles. The self-assembly of this new type of nanoparticles is ...Here we show the encapsulation of 35 nm diameter, nearly-spherical, DNA origami by self-assembly of SV40-like (simian virus 40) particles. The self-assembly of this new type of nanoparticles is highly reproducible and efficient. The structure of these particles was determined by cryo-EM. The capsid forms a regular SV40 lattice of T = 7d icosahedral symmetry and the structural features of encapsulated DNA origami are fully visible. These particles are a promising biomaterial for use in various medical applications.
History
DepositionMar 1, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseMay 1, 2019-
UpdateJun 12, 2019-
Current statusJun 12, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4651.png

Downloads & links

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Map

FileDownload / File: emd_4651.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSphere DNA origami encapsulated by SV40 VP1 capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 300 pix.
= 690. Å		2.3 Å/pix.
x 300 pix.
= 690. Å		2.3 Å/pix.
x 300 pix.
= 690. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.01805626 - 0.057950035
Average (Standard dev.)0.004601249 (±0.009882957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 690.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z690.000690.000690.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0180.0580.005

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Supplemental data

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Sample components

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Entire : Simian virus 40

EntireName: Simian virus 40
Components
  • Virus: Simian virus 40

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Supramolecule #1: Simian virus 40

SupramoleculeName: Simian virus 40 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10633 / Sci species name: Simian virus 40 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host systemOrganism: Spodoptera frugiperda (fall armyworm)

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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: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
DetailsFor assembly reactions, commercially available DNA origami structure was incubated with disassembled VP1 pentamers in assembly buffer at room temperature for 24 hours.

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta2) / Number images used: 7939
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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