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Yorodumi- PDB-7r6m: Post-2S intermediate of the Tetrahymena group I intron, symmetry-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r6m | ||||||||||||||||||
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Title | Post-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | ||||||||||||||||||
Components |
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Keywords | RNA / Ribozyme / Group I intron / catalytic RNA | ||||||||||||||||||
Function / homology | : / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å | ||||||||||||||||||
Authors | Thelot, F. / Liu, D. / Liao, M. / Yin, P. | ||||||||||||||||||
Funding support | United States, 5items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r6m.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r6m.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 7r6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/7r6m ftp://data.pdbj.org/pub/pdb/validation_reports/r6/7r6m | HTTPS FTP |
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-Related structure data
Related structure data | 24282MC 7r6lC 7r6nC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: RNA chain | Mass: 128011.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) / References: GenBank: V01416 | ||
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#2: DNA/RNA hybrid | Mass: 4356.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) | ||
#3: Chemical | ChemComp-MG / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Post-2S intermediate of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct Type: COMPLEX / Entity ID: #1-#2 / Source: SYNTHETIC | |||||||||||||||
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Molecular weight | Value: 0.13 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 105000 X / Cs: 2.7 mm |
Image recording | Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113548 / Symmetry type: POINT |