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Yorodumi- PDB-8bu8: Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bu8 | ||||||
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Title | Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT) | ||||||
Components | RNA (354-MER) | ||||||
Keywords | RNA / RNA origami / Nanostructure / self-assembly | ||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.56 Å | ||||||
Authors | Sampedro, N. / Andersen, E.S. / McRae, E.K.S. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Small / Year: 2023 Title: An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly. Authors: Néstor Sampedro Vallina / Ewan K S McRae / Cody Geary / Ebbe Sloth Andersen / Abstract: RNA nanotechnology takes advantage of structural modularity to build self-assembling nano-architectures with applications in medicine and synthetic biology. The use of paranemic motifs, that form ...RNA nanotechnology takes advantage of structural modularity to build self-assembling nano-architectures with applications in medicine and synthetic biology. The use of paranemic motifs, that form without unfolding existing secondary structure, allows for the creation of RNA nanostructures that are compatible with cotranscriptional folding in vitro and in vivo. In previous work, kissing-loop (KL) motifs have been widely used to design RNA nanostructures that fold cotranscriptionally. However, the paranemic crossover (PX) motif has not yet been explored for cotranscriptional RNA origami architectures and information about the structural geometry of the motif is unknown. Here, a six base pair-wide paranemic RNA interaction that arranges double helices in a perpendicular manner is introduced, allowing for the generation of a new and versatile building block: the paranemic-crossover triangle (PXT). The PXT is self-assembled by cotranscriptional folding and characterized by cryogenic electron microscopy, revealing for the first time an RNA PX interaction in high structural detail. The PXT is used as a building block for the construction of multimers that form filaments and rings and a duplicated PXT motif is used as a building block to self-assemble cubic structures, demonstrating the PXT as a rigid self-folding domain for the development of wireframe RNA origami architectures. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bu8.cif.gz | 174 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bu8.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 8bu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bu8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8bu8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8bu8_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 8bu8_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/8bu8 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/8bu8 | HTTPS FTP |
-Related structure data
Related structure data | 16245MC 8btzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: RNA chain | Mass: 113647.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: In vitro transcribed RNA / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT) Type: COMPLEX / Details: In vitro transcribed RNA purified by SEC. / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 113.63 kDa/nm / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: synthetic construct (others) | ||||||||||||||||||||
Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample was purified by size exclusion chromatography and concentrated in an Amicon spin concentrator. | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 294 K Details: 3 microliter droplet, 4 second delay before blotting, 6 second blot, 0 second delay before plunging. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Details: Patch CTF estimation (multi) from cryoSPARC. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
3D reconstruction | Resolution: 6.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128507 / Symmetry type: POINT |