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- EMDB-41656: RNA origami 3-helix tile Traptamer -

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Basic information

Entry
Database: EMDB / ID: EMD-41656
TitleRNA origami 3-helix tile Traptamer
Map data
Sample
  • Complex: 14-14 Traptamer
    • RNA: RNA (363-MER)
KeywordsOrigami / aptamer / switch / sensor / toe-hold / robot / broccoli / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.94 Å
AuthorsMcRae EKS / Vallina NS / Andersen ES
Funding supportEuropean Union, Denmark, Canada, 6 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765703European Union
Independent Research Fund Denmark - Technology and Production Sciences9040-00425B Denmark
Natural Sciences and Engineering Research Council (NSERC, Canada)532417 Canada
The Carlsberg FoundationCF20-0635 Denmark
European Research Council (ERC)683305European Union
Novo Nordisk Foundation0060694 Denmark
CitationJournal: 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
DepositionAug 18, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41656.png

Downloads & links

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Map

FileDownload / File: emd_41656.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.294 Å
Density
Contour LevelBy AUTHOR: 0.0846
Minimum - Maximum-0.02636311 - 0.370288
Average (Standard dev.)0.000029233355 (±0.011831472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.264 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41656_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Additional map: #1

Fileemd_41656_additional_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_41656_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

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Half map: #1

Fileemd_41656_half_map_2.map
Projections & Slices
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Sample components

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Entire : 14-14 Traptamer

EntireName: 14-14 Traptamer
Components
  • Complex: 14-14 Traptamer
    • RNA: RNA (363-MER)

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Supramolecule #1: 14-14 Traptamer

SupramoleculeName: 14-14 Traptamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: An RNA origami 3 helix tile with an inactive broccoli aptamer in the central helix.
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: RNA (363-MER)

MacromoleculeName: RNA (363-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 116.977742 KDa
SequenceString: GGAAUCUCGC CCGAUGUUCG CAUCGGGAUU UGCAGGUCCA UGGAUUACAC CAUGCAACGC AGACCUGUAG AUGCCACGCU AGCCGUGGU GAGGGUCGGG UCCAGAUGUC AUUCGACUUU AACGCGCCUA AGCGUUGAAG GCGUGUUAGA GCAGAUAGUU C GCUAUCUG ...String:
GGAAUCUCGC CCGAUGUUCG CAUCGGGAUU UGCAGGUCCA UGGAUUACAC CAUGCAACGC AGACCUGUAG AUGCCACGCU AGCCGUGGU GAGGGUCGGG UCCAGAUGUC AUUCGACUUU AACGCGCCUA AGCGUUGAAG GCGUGUUAGA GCAGAUAGUU C GCUAUCUG GGGAGCCUGU UCGCAGGCUC AGGAGCCUUC GGGCUCCUAG CGCUAUUACC CCGGACACCA CCGGGCAGAC AA GUAAUGG UGCUCCUCGA AUGACUUCUG UUGAGUAGAG UGUGGGCUCC GCGGCUAGUG UGCACCUUAG CGGUGAAUGU CUG ACACCG UUAAGGUGGU UACUCUUCGG AGUAACGCCG AGAUUCC

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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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
40.0 mMHEPES
50.0 mMKCLPotassium Chloride
5.0 mMMgCl2Magnesium Chloride
GridMaterial: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: LEICA EM GP / Details: Protochips Au-Flat 1.2/1.3 grids..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2 / Details: Pixel size of 0.645 A/px
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 220000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ob3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: OTHER
Output model

PDB-8tvz:
RNA origami 3-helix tile Traptamer

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