+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41312 | |||||||||
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Title | Tetrahymena Ribozyme scaffolded Fluoride riboswitch | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribozyme / xrRNA / Scaffold / RNA | |||||||||
Biological species | Tetrahymena (eukaryote) / Thermotoga petrophila (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Langeberg CJ / Kieft JS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM. Authors: Conner J Langeberg / Jeffrey S Kieft / Abstract: Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules (≤50 kDa) remain challenging targets due to their ...Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules (≤50 kDa) remain challenging targets due to their intrinsic low signal to noise ratio. Methods to help resolve small proteins have been applied but development of similar approaches to aid in structural determination of small, structured RNA elements have lagged. Here, we present a scaffold-based approach that we used to recover maps of sub-25 kDa RNA domains to 4.5-5.0 Å. While lacking the detail of true high-resolution maps, these maps are suitable for model building and preliminary structure determination. We demonstrate this method helped faithfully recover the structure of several RNA elements of known structure, and that it promises to be generalized to other RNAs without disturbing their native fold. This approach may streamline the sample preparation process and reduce the optimization required for data collection. This first-generation scaffold approach provides a robust system to aid in RNA structure determination by cryo-EM and lays the groundwork for further scaffold optimization to achieve higher resolution. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41312.map.gz | 256.9 MB | EMDB map data format | |
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Header (meta data) | emd-41312-v30.xml emd-41312.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41312_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_41312.png | 55.4 KB | ||
Filedesc metadata | emd-41312.cif.gz | 5.2 KB | ||
Others | emd_41312_half_map_1.map.gz emd_41312_half_map_2.map.gz | 474.5 MB 474.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41312 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41312 | HTTPS FTP |
-Validation report
Summary document | emd_41312_validation.pdf.gz | 772.2 KB | Display | EMDB validaton report |
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Full document | emd_41312_full_validation.pdf.gz | 771.8 KB | Display | |
Data in XML | emd_41312_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | emd_41312_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41312 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41312 | HTTPS FTP |
-Related structure data
Related structure data | 8tjvMC 8tjqC 8tjuC 8tjxC M: atomic model generated by this map 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_41312.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41312_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41312_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tetrahymena Ribozyme scaffolded Fluoride riboswitch
Entire | Name: Tetrahymena Ribozyme scaffolded Fluoride riboswitch |
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Components |
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-Supramolecule #1: Tetrahymena Ribozyme scaffolded Fluoride riboswitch
Supramolecule | Name: Tetrahymena Ribozyme scaffolded Fluoride riboswitch / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Tetrahymena (eukaryote) |
-Macromolecule #1: RNA (417-MER)
Macromolecule | Name: RNA (417-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Thermotoga petrophila (bacteria) |
Molecular weight | Theoretical: 134.830641 KDa |
Sequence | String: GGGCGAUGAG GCCCGCCCAA ACUGCCCUAU AUGGAUGCAG UUCACAGACU AAAUGUCGGU CGGGGAAGAU GUAUUCUUCU CAUAAGAUA UAGUCGGACC UCUCCUUAAU GGGAGCUAGC GGAUGAAGUG AUGCAACACU GGAGCCGCUG GGAACUAAUU U GUAUGCGA ...String: GGGCGAUGAG GCCCGCCCAA ACUGCCCUAU AUGGAUGCAG UUCACAGACU AAAUGUCGGU CGGGGAAGAU GUAUUCUUCU CAUAAGAUA UAGUCGGACC UCUCCUUAAU GGGAGCUAGC GGAUGAAGUG AUGCAACACU GGAGCCGCUG GGAACUAAUU U GUAUGCGA AAGUAUAUUG AUUAGUUUUG GAGGAGGGAA AAGUUAUCAG GCAUGCACCU GGUAGCUAGU CUUUAAACCA AU AGAUUGC AUCGGUUUAA AAGGCAAGAC CGUCAAAUUG CGGGAAAGGG GUCAACAGCC GUUCAGUACC AAGUCUCAGG GGA AACUUU GAGAUGGCCU UGCAAAGGGU AUGGUAAUAA GCUGACGGAC AUGGUCCUAA CCACGCAGCC AAGUCCUAAG UAGG GCUGA UGGCCUCUAC UG |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 30 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: FLUORIDE ION
Macromolecule | Name: FLUORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: F |
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Molecular weight | Theoretical: 18.998 Da |
Chemical component information | ChemComp-F: |
-Macromolecule #4: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 6 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |