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- EMDB-21026: Truncated Tetrahedral RNA Nanostructures -

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Basic information

Entry
Database: EMDB / ID: EMD-21026
TitleTruncated Tetrahedral RNA Nanostructures
Map data
Sample
  • Complex: Tetrahedral RNA nanoparticle
Biological speciesunidentified, produced by invitro transcription of synthetic templates (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsWu W / Zakrevsky P / Heinz W / Khant H / Kasprzak WK / Bindewald E / Dorjsuren N / Fields E / De Val N / Jaeger L / Shapiro BA
CitationJournal: Nanoscale / Year: 2020
Title: Truncated tetrahedral RNA nanostructures exhibit enhanced features for delivery of RNAi substrates.
Authors: Paul Zakrevsky / Wojciech K Kasprzak / William F Heinz / Weimin Wu / Htet Khant / Eckart Bindewald / Nomongo Dorjsuren / Eric A Fields / Natalia de Val / Luc Jaeger / Bruce A Shapiro /
Abstract: Using RNA as a material for nanoparticle construction provides control over particle size and shape at the nano-scale. RNA nano-architectures have shown promise as delivery vehicles for RNA ...Using RNA as a material for nanoparticle construction provides control over particle size and shape at the nano-scale. RNA nano-architectures have shown promise as delivery vehicles for RNA interference (RNAi) substrates, allowing multiple functional entities to be combined on a single particle in a programmable fashion. Rather than employing a completely bottom-up approach to scaffold design, here multiple copies of an existing synthetic supramolecular RNA nano-architecture serve as building blocks along with additional motifs for the design of a novel truncated tetrahedral RNA scaffold, demonstrating that rationally designed RNA assemblies can themselves serve as modular pieces in the construction of larger rationally designed structures. The resulting tetrahedral scaffold displays enhanced characteristics for RNAi-substrate delivery in comparison to similar RNA-based scaffolds, as evidenced by its increased functional capacity, increased cellular uptake and ultimately an increased RNAi efficacy of its adorned Dicer substrate siRNAs. The unique truncated tetrahedral shape of the nanoparticle core appears to contribute to this particle's enhanced function, indicating the physical characteristics of RNA scaffolds merit significant consideration when designing platforms for delivery of functional RNAs via RNA nanoparticles.
History
DepositionNov 22, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseFeb 5, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21026.png

Downloads & links

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Map

FileDownload / File: emd_21026.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.0018489175 - 0.021540685
Average (Standard dev.)0.00016715552 (±0.0018350774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z348.160348.160348.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0020.0220.000

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Supplemental data

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Sample components

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Entire : Tetrahedral RNA nanoparticle

EntireName: Tetrahedral RNA nanoparticle
Components
  • Complex: Tetrahedral RNA nanoparticle

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Supramolecule #1: Tetrahedral RNA nanoparticle

SupramoleculeName: Tetrahedral RNA nanoparticle / type: complex / ID: 1 / Parent: 0
Details: Supra-molecular RNA structure assembled from rationally designed RNA strands produced by in vitro transcription of synthetic DNA templates
Source (natural)Organism: unidentified, produced by invitro transcription of synthetic templates (unknown)

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8862
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8862
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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