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- PDB-7ygd: Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ygd | ||||||
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Title | Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing | ||||||
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![]() | RNA / Tetrahymena ribozyme / second step of self-splicing / conformation 1 | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å | ||||||
![]() | Li, S. / Michael, Z.P. / Zhang, X. / Greg, P. / Zhang, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM. Authors: Shanshan Li / Michael Z Palo / Xiaojing Zhang / Grigore Pintilie / Kaiming Zhang / ![]() ![]() Abstract: Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self- ...Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self-splicing reactions, we determine the structures of L-16 Tetrahymena ribozyme in complex with a 5'-splice site analog product and a 3'-splice site analog substrate using cryo-EM. We solve six conformations from a single specimen, corresponding to different splicing intermediates after the first ester-transfer reaction. The structures reveal dynamics during self-splicing, including large conformational changes of the internal guide sequence and the J5/4 junction as well as subtle rearrangements of active-site metals and the hydrogen bond formed between the 2'-OH group of A261 and the N2 group of guanosine substrate. These results help complete a detailed structural and mechanistic view of this paradigmatic group I intron undergoing the second step of self-splicing. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.6 KB | Display | ![]() |
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PDB format | ![]() | 142.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33816MC ![]() 7yg8C ![]() 7yg9C ![]() 7ygaC ![]() 7ygbC ![]() 7ygcC 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: 911.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
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#2: RNA chain | Mass: 1788.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#3: RNA chain | Mass: 127011.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: in vitro transcription vector pT7-Fluc(deltai) (others) References: GenBank: 10832 | ||
#4: 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 |
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Sample preparation
Component | Name: Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.13 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: in vitro transcription vector pT7-Fluc(deltai) (others) |
Buffer solution | pH: 8 |
Specimen | Conc.: 2.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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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: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 52.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
Particle selection | Num. of particles selected: 4255846 | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57096 / Symmetry type: POINT |