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- EMDB-16077: Inner helical shell of CCMV capsid protein on DNA origami 6HB-10k -

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Basic information

Entry
Database: EMDB / ID: EMD-16077
TitleInner helical shell of CCMV capsid protein on DNA origami 6HB-10k
Map data
Sample
  • Complex: Inner helical shell of CCMV capsid protein on DNA origami 6HB-10k
Keywordsorigami / capsid / VIRUS LIKE PARTICLE
Biological speciesCowpea chlorotic mottle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsKumpula E-P / Seitz I / Kostiainen MA / Huiskonen JT
Funding supportEuropean Union, Finland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101002258European Union
Academy of Finland341057 Finland
CitationJournal: Nat Nanotechnol / Year: 2023
Title: DNA-origami-directed virus capsid polymorphism.
Authors: Iris Seitz / Sharon Saarinen / Esa-Pekka Kumpula / Donna McNeale / Eduardo Anaya-Plaza / Vili Lampinen / Vesa P Hytönen / Frank Sainsbury / Jeroen J L M Cornelissen / Veikko Linko / Juha T ...Authors: Iris Seitz / Sharon Saarinen / Esa-Pekka Kumpula / Donna McNeale / Eduardo Anaya-Plaza / Vili Lampinen / Vesa P Hytönen / Frank Sainsbury / Jeroen J L M Cornelissen / Veikko Linko / Juha T Huiskonen / Mauri A Kostiainen /
Abstract: Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have ...Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA-DNA origami structures to pave way for next-generation cargo protection and targeting strategies.
History
DepositionNov 1, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16077.png

Downloads & links

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Map

FileDownload / File: emd_16077.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-4.167532 - 13.772358000000001
Average (Standard dev.)0.023570597 (±1.5605692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 491.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16077_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_16077_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16077_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Inner helical shell of CCMV capsid protein on DNA origami 6HB-10k

EntireName: Inner helical shell of CCMV capsid protein on DNA origami 6HB-10k
Components
  • Complex: Inner helical shell of CCMV capsid protein on DNA origami 6HB-10k

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Supramolecule #1: Inner helical shell of CCMV capsid protein on DNA origami 6HB-10k

SupramoleculeName: Inner helical shell of CCMV capsid protein on DNA origami 6HB-10k
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Cowpea chlorotic mottle virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
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: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 32473
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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