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Yorodumi- EMDB-16245: Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16245 | |||||||||
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Title | Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA origami / Nanostructure / self-assembly / RNA | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.56 Å | |||||||||
Authors | Sampedro N / Andersen ES / McRae EKS | |||||||||
Funding support | Denmark, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16245.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-16245-v30.xml emd-16245.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_16245.png | 31.7 KB | ||
Filedesc metadata | emd-16245.cif.gz | 5.2 KB | ||
Others | emd_16245_half_map_1.map.gz emd_16245_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16245 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16245 | HTTPS FTP |
-Validation report
Summary document | emd_16245_validation.pdf.gz | 801.3 KB | Display | EMDB validaton report |
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Full document | emd_16245_full_validation.pdf.gz | 800.8 KB | Display | |
Data in XML | emd_16245_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_16245_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16245 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16245 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16245.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: 1.62 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-A
File | emd_16245_half_map_1.map | ||||||||||||
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Annotation | Half-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-B
File | emd_16245_half_map_2.map | ||||||||||||
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Annotation | Half-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT)
Entire | Name: Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT) |
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Components |
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-Supramolecule #1: Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT)
Supramolecule | Name: Double-motif Single-stranded Paranemic Crossover RNA Triangle (2PXT) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: In vitro transcribed RNA purified by SEC. |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 113.63 kDa/nm |
-Macromolecule #1: RNA (354-MER)
Macromolecule | Name: RNA (354-MER) / type: rna / ID: 1 / Details: In vitro transcribed RNA / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 113.647586 KDa |
Sequence | String: GUUACUCACC UCUUCGGAGA AAACGGUCCG AGCGUGGUUC GCCACUAAAA UACCGUUUUG GCCUGAAUGU GUCUGGUCCU UCCGCAGCC GUUUGAUGAG UUCGCUCAUC AUAGCGGGCU UACCAAACAG UUCGCUGCCA CCGUGCGGAA GCAGUUUCGA C UGAUAGAU ...String: GUUACUCACC UCUUCGGAGA AAACGGUCCG AGCGUGGUUC GCCACUAAAA UACCGUUUUG GCCUGAAUGU GUCUGGUCCU UCCGCAGCC GUUUGAUGAG UUCGCUCAUC AUAGCGGGCU UACCAAACAG UUCGCUGCCA CCGUGCGGAA GCAGUUUCGA C UGAUAGAU CACGGUGGGA CUAUUCGUAG UCUUUGGUGA GCUCGUUACG UUUCUUCGGA AACGAACGGC UGAUCUAUGA CC AGAUGUA UUCAGGCCGU GAGUAACGUC GCCGUACAUC UUCGGAUGUA GCGUCCCUAU UUUACAAACU UCGGUUUGGC UCG GAGGGA CGCAGCAGGG UUCGCCCUGC UCGGCGAC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 294 K Details: 3 microliter droplet, 4 second delay before blotting, 6 second blot, 0 second delay before plunging.. | ||||||||||||
Details | Sample was purified by size exclusion chromatography and concentrated in an Amicon spin concentrator. |
-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) / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 128507 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) |