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Yorodumi- EMDB-40393: Tertiary structure of an individual particle of self-folding RNA ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40393 | ||||||||||||||||||
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Title | Tertiary structure of an individual particle of self-folding RNA polymer (particle #159) | ||||||||||||||||||
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Sample |
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Keywords | Single molecule structure / Individual Particle cryo-Electron Tomography / IPET / Cryo-ET / tertiary structure / Structural Flexibility / Self-folding mechanism / RNA origami / RNA | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | electron tomography / cryo EM / Resolution: 25.0 Å | ||||||||||||||||||
Authors | Liu J / Ren G | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: To Be Published Title: Tertiary Structure of an Individual Particle of Self-folding RNA Polymer Authors: Liu J / McRae EKS / Zhang M / Geary C / Andersen ES / Ren G | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40393.map.gz | 9.1 MB | EMDB map data format | |
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Header (meta data) | emd-40393-v30.xml emd-40393.xml | 12 KB 12 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40393_fsc.xml | 6.1 KB | Display | FSC data file |
Images | emd_40393.png | 78.2 KB | ||
Filedesc metadata | emd-40393.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40393 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40393 | HTTPS FTP |
-Validation report
Summary document | emd_40393_validation.pdf.gz | 305.6 KB | Display | EMDB validaton report |
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Full document | emd_40393_full_validation.pdf.gz | 305.2 KB | Display | |
Data in XML | emd_40393_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_40393_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40393 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40393 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40393.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : RNA Origami 6 Helix Bundle with Clasp (6HBC)
Entire | Name: RNA Origami 6 Helix Bundle with Clasp (6HBC) |
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Components |
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-Supramolecule #1: RNA Origami 6 Helix Bundle with Clasp (6HBC)
Supramolecule | Name: RNA Origami 6 Helix Bundle with Clasp (6HBC) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The RNA was transcribed from linearized DNA template using T7 RNA polymerase purified in house. |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 230 KDa |
-Macromolecule #1: RNA Origami 6 Helix Bundle with Clasp (6HBC)
Macromolecule | Name: RNA Origami 6 Helix Bundle with Clasp (6HBC) / type: rna / ID: 1 |
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Sequence | String: GGGAGAGUAC UAUUCAGAUG CAGACCGCAA GUUCAGAGCG GUUUGCAUCU AGGGUACGUU UUCGAACGUA UCCUCCGACU AAGUGUAUUC GUAUACUUAG UGCCUUGUGC CUGCUUCGGC AGGCAUGACC CAAAUGUGCC UUUCGGGGCA CAUUUCCGGU CAUCCAAGUU ...String: GGGAGAGUAC UAUUCAGAUG CAGACCGCAA GUUCAGAGCG GUUUGCAUCU AGGGUACGUU UUCGAACGUA UCCUCCGACU AAGUGUAUUC GUAUACUUAG UGCCUUGUGC CUGCUUCGGC AGGCAUGACC CAAAUGUGCC UUUCGGGGCA CAUUUCCGGU CAUCCAAGUU CGCUUGGGUG AUGCGGGCGU AUAGGUUCGU CUAUACGUCC GCGUUUUCCG AGAAGAGGUA ACUCGGGAAA CCGGUCCACG UGACAAAGGU AGAGUUACGU GGAGGGAGCA GCUGCAAAGG GAUAAUGCAG UUGCUGGCUG GAUGCCAGAA CUCACGACUG GCAUCUACGG GGAUGGUGCU CUCCCAAUUC UCCAUUUACC GCCGAAUCGA CCCCAACGUG AGAGGGGUCG GUUCCCCGAG CAUAGACCAA UAUCCCAGGU UUAUGCUCCC CAACGCUGGA CGAACUACCU ACGUCUAGCG UUCCGGCAAA UGAGUCAAUA CCUCAGACUU AUUUGCGGUG CCUGAGCCUA AACUGAACAU GGGUUCAGGC AUCUUGGCUC CAGUUCGCUG GAGCCGACGG UAGCGCUGCG UUCGCGCAGU GCUAGGGAGC AUCCGUUUUC GAGCGGAUGC UGGGCGGUUG CCUGUUCGCA GGCAAUCGGG CCUACUCAUG AUUCGUCAUG AGUGGUGACA GCGUGAUGUU CGCAUUACGC UGUCGGGUAG AUGGAGAAUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP | ||||||||||||
Details | In vitro transcribed RNA was purified by size exclusion chromatography and spin concentrated in amicon spin columns. | ||||||||||||
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 21 / Average exposure time: 7.39 sec. / Average electron dose: 21.5 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: 2.0 µm / Nominal magnification: 53000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |