+Open data
-Basic information
Entry | Database: PDB / ID: 8tvz | |||||||||||||||||||||
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Title | RNA origami 3-helix tile Traptamer | |||||||||||||||||||||
Components | RNA (363-MER) | |||||||||||||||||||||
Keywords | RNA / Origami / aptamer / switch / sensor / toe-hold / robot / broccoli | |||||||||||||||||||||
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: 5.94 Å | |||||||||||||||||||||
Authors | McRae, E.K.S. / Vallina, N.S. / Andersen, E.S. | |||||||||||||||||||||
Funding support | European Union, Denmark, Canada, 6items
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Citation | Journal: Sci Adv / Year: 2024 Title: An RNA origami robot that traps and releases a fluorescent aptamer. Authors: Néstor Sampedro Vallina / Ewan K S McRae / Cody Geary / Ebbe S Andersen / Abstract: RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA ...RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA robotic devices that both sense, compute, and actuate to obtain enhanced control over molecular processes. Here, we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer," that mechanically traps the fluorescent aptamer, iSpinach. The Traptamer is shown to sense two RNA key strands, acts as a Boolean AND gate, and reversibly controls the fluorescence of the iSpinach aptamer. Cryo-electron microscopy of the closed Traptamer structure at 5.45-angstrom resolution reveals the mechanical mode of distortion of the iSpinach motif. Our study suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA machines that through sensing, computing, and actuation modules can be used to precisely control RNA functionalities in cellular systems. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tvz.cif.gz | 218.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tvz.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 8tvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tvz_validation.pdf.gz | 981.5 KB | Display | wwPDB validaton report |
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Full document | 8tvz_full_validation.pdf.gz | 994.1 KB | Display | |
Data in XML | 8tvz_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 8tvz_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/8tvz ftp://data.pdbj.org/pub/pdb/validation_reports/tv/8tvz | HTTPS FTP |
-Related structure data
Related structure data | 41656MC 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: 116977.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) 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: 14-14 Traptamer / Type: COMPLEX Details: An RNA origami 3 helix tile with an inactive broccoli aptamer in the central helix. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: synthetic construct (others) | ||||||||||||||||||||
Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 15mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K / Details: Protochips Au-Flat 1.2/1.3 grids. |
-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 defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Details: Pixel size of 0.645 A/px |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
3D reconstruction | Resolution: 5.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220000 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: OTHER | |||||||||||||||||||||
Atomic model building | PDB-ID: 5OB3 Accession code: 5OB3 / Source name: PDB / Type: experimental model |