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- EMDB-34058: rO44 A-form (staple xover asymmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-34058
TitlerO44 A-form (staple xover asymmetry)
Map datarO44 A-form (staple xover asymmetry)
Sample
  • Complex: rO44 A-form (staple xover asymmetry)
Biological speciesInovirus M13
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsZhang K / Li S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
CitationJournal: Nat Commun / Year: 2023
Title: 3D RNA-scaffolded wireframe origami.
Authors: Molly F Parsons / Matthew F Allan / Shanshan Li / Tyson R Shepherd / Sakul Ratanalert / Kaiming Zhang / Krista M Pullen / Wah Chiu / Silvi Rouskin / Mark Bathe /
Abstract: Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite ...Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
History
DepositionAug 9, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34058.png

Downloads & links

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Map

FileDownload / File: emd_34058.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationrO44 A-form (staple xover asymmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 240 pix.
= 480. Å		2 Å/pix.
x 240 pix.
= 480. Å		2 Å/pix.
x 240 pix.
= 480. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.49
Minimum - Maximum-0.2361251 - 1.4291546
Average (Standard dev.)0.0040411125 (±0.09033755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34058_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34058_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : rO44 A-form (staple xover asymmetry)

EntireName: rO44 A-form (staple xover asymmetry)
Components
  • Complex: rO44 A-form (staple xover asymmetry)

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Supramolecule #1: rO44 A-form (staple xover asymmetry)

SupramoleculeName: rO44 A-form (staple xover asymmetry) / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Inovirus M13

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.3) / Number images used: 22340
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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