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Yorodumi- EMDB-24281: 5 prime exon-free pre-2S intermediate of the Tetrahymena group I ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24281 | ||||||||||||||||||
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Title | 5 prime exon-free pre-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | ||||||||||||||||||
Map data | 5 prime exon-free pre-2S intermediate of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | ||||||||||||||||||
Sample |
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Keywords | Ribozyme / Group I intron / catalytic RNA / RNA | ||||||||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | ||||||||||||||||||
Authors | Thelot F / Liu D | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Methods / Year: 2022 Title: Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Authors: Di Liu / François A Thélot / Joseph A Piccirilli / Maofu Liao / Peng Yin / Abstract: High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural ...High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural determination of RNA-only structures using single-particle cryogenic electron microscopy (cryo-EM). This strategy-ROCK (RNA oligomerization-enabled cryo-EM via installing kissing loops)-involves installing kissing-loop sequences onto the functionally nonessential stems of RNAs for homomeric self-assembly into closed rings with multiplied molecular weights and mitigated structural flexibility. ROCK enables cryo-EM reconstruction of the Tetrahymena group I intron at 2.98-Å resolution overall (2.85 Å for the core), allowing de novo model building of the complete RNA, including the previously unknown peripheral domains. ROCK is further applied to two smaller RNAs-the Azoarcus group I intron and the FMN riboswitch, revealing the conformational change of the former and the bound ligand in the latter. ROCK holds promise to greatly facilitate the use of cryo-EM in RNA structural studies. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24281.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-24281-v30.xml emd-24281.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_24281.png | 106.5 KB | ||
Filedesc metadata | emd-24281.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24281 | HTTPS FTP |
-Validation report
Summary document | emd_24281_validation.pdf.gz | 470.2 KB | Display | EMDB validaton report |
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Full document | emd_24281_full_validation.pdf.gz | 469.8 KB | Display | |
Data in XML | emd_24281_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_24281_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24281 | HTTPS FTP |
-Related structure data
Related structure data | 7r6lMC 7r6mC 7r6nC 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_24281.map.gz / Format: CCP4 / Size: 7.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 5 prime exon-free pre-2S intermediate of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : 5 prime exon-free pre-2S intermediate of Tetrahymena group I intr...
Entire | Name: 5 prime exon-free pre-2S intermediate of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct |
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Components |
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-Supramolecule #1: 5 prime exon-free pre-2S intermediate of Tetrahymena group I intr...
Supramolecule | Name: 5 prime exon-free pre-2S intermediate of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Synthetically produced: Yes |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: Group I intron, 5 prime fragment
Macromolecule | Name: Group I intron, 5 prime fragment / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 121.342711 KDa |
Sequence | String: GGCCGGGUGG AGGGAAAAGU UAUCAGGCAU GCACCUGGUA GCUAGUCUUU AAACCAAUAG AUUGCAUCGG UUUAAAAGGC AAGACCGUC AAAUUGCGGG AAAGGGGUCA ACAGCCGUUC AGUACCAAGU CUCAGGGGAA ACUUUGAGAU GGCCUUGCAA A GGGUAUGG ...String: GGCCGGGUGG AGGGAAAAGU UAUCAGGCAU GCACCUGGUA GCUAGUCUUU AAACCAAUAG AUUGCAUCGG UUUAAAAGGC AAGACCGUC AAAUUGCGGG AAAGGGGUCA ACAGCCGUUC AGUACCAAGU CUCAGGGGAA ACUUUGAGAU GGCCUUGCAA A GGGUAUGG UAAUAAGCUG ACGGACAUGG UCCUAACCAC GCAGCCAAGU CCUAAGUCAA GGAUGGUUCU UGAUAUGGAU GC AGUUCAC AGACUAAAUG UCGGUCGGGG AAGAGAACCA UCCUCUUCUC AUAAGAUAUA GUCGGACCUC UCCUUAAUGG GAG CUAGCG GAUGAAGUGA UGCAACACUG GAGCCGCUGG GAACUAAUUU GUAUGCGAA GENBANK: GENBANK: V01416.1 |
-Macromolecule #2: Group I intron, 3 prime fragment plus 3 prime exon
Macromolecule | Name: Group I intron, 3 prime fragment plus 3 prime exon / type: other / ID: 2 / Number of copies: 1 Classification: polydeoxyribonucleotide/polyribonucleotide hybrid |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 11.803012 KDa |
Sequence | String: AGUAUAUUGA UUAGUUUUGG AGUACUC(DG)(DA)C CCGGCCA GENBANK: GENBANK: V01416.1 |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 20 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 105000 |
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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82575 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |