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- PDB-7r6n: Exon-free state of the Tetrahymena group I intron, symmetry-expan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r6n | ||||||||||||||||||
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Title | Exon-free state of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct | ||||||||||||||||||
![]() | Group I intron![]() | ||||||||||||||||||
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Function / homology | ![]() ![]() ![]() | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Thelot, F. / Liu, D. / Liao, M. / Yin, P. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178 KB | Display | ![]() |
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PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 24283MC ![]() 7r6lC ![]() 7r6mC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: RNA chain | ![]() Mass: 127005.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct Type: COMPLEX / Entity ID: #1 / Source: SYNTHETIC | |||||||||||||||
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Molecular weight | Value: 0.13 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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![]() ![]() |
Electron lens | Mode: OTHER / Nominal magnification: 105000 X / Cs![]() |
Image recording | Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction![]() | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85596 / Symmetry type: POINT |