+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41656 | |||||||||||||||||||||
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Title | RNA origami 3-helix tile Traptamer | |||||||||||||||||||||
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Sample |
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Keywords | Origami / aptamer / switch / sensor / toe-hold / robot / broccoli / RNA | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.94 Å | |||||||||||||||||||||
Authors | McRae EKS / Vallina NS / Andersen ES | |||||||||||||||||||||
Funding support | European Union, Denmark, Canada, 6 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41656.map.gz | 31.4 MB | EMDB map data format | |
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Header (meta data) | emd-41656-v30.xml emd-41656.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41656_fsc.xml | 9.6 KB | Display | FSC data file |
Images | emd_41656.png | 70 KB | ||
Masks | emd_41656_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-41656.cif.gz | 5.5 KB | ||
Others | emd_41656_additional_1.map.gz emd_41656_half_map_1.map.gz emd_41656_half_map_2.map.gz | 57.5 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41656 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41656 | HTTPS FTP |
-Validation report
Summary document | emd_41656_validation.pdf.gz | 717 KB | Display | EMDB validaton report |
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Full document | emd_41656_full_validation.pdf.gz | 716.5 KB | Display | |
Data in XML | emd_41656_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_41656_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41656 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41656 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41656.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.294 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41656_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_41656_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_41656_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41656_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 14-14 Traptamer
Entire | Name: 14-14 Traptamer |
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Components |
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-Supramolecule #1: 14-14 Traptamer
Supramolecule | Name: 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. |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: RNA (363-MER)
Macromolecule | Name: RNA (363-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 116.977742 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: LEICA EM GP / Details: Protochips Au-Flat 1.2/1.3 grids.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |