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Yorodumi- PDB-7yc8: Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yc8 | ||||||
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Title | Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicing | ||||||
Components | RNA (388-MER) | ||||||
Keywords | RNA / Tetrahymena ribozyme / first step of self-splicing / conformation 1 | ||||||
Function / homology | GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Tetrahymena (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.14 Å | ||||||
Authors | Zhang, X. / Li, S. / Pintilie, G. / Palo, M.Z. / Zhang, K. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Snapshots of the first-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM. Authors: Xiaojing Zhang / Shanshan Li / Grigore Pintilie / Michael Z Palo / Kaiming Zhang / Abstract: Tetrahymena ribozyme is a group I intron, whose self-splicing is the result of two sequential ester-transfer reactions. To understand how it facilitates catalysis in the first self-splicing reaction, ...Tetrahymena ribozyme is a group I intron, whose self-splicing is the result of two sequential ester-transfer reactions. To understand how it facilitates catalysis in the first self-splicing reaction, we used cryogenic electron microscopy (cryo-EM) to resolve the structures of L-16 Tetrahymena ribozyme complexed with a 11-nucleotide 5'-splice site analog substrate. Four conformations were achieved to 4.14, 3.18, 3.09 and 2.98 Å resolutions, respectively, corresponding to different splicing intermediates during the first enzymatic reaction. Comparison of these structures reveals structural alterations, including large conformational changes in IGS/IGSext (P1-P1ext duplex) and J5/4, as well as subtle local rearrangements in the G-binding site. These structural changes are required for the enzymatic activity of the Tetrahymena ribozyme. Our study demonstrates the ability of cryo-EM to capture dynamic RNA structural changes, ushering in a new era in the analysis of RNA structure-function by cryo-EM. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yc8.cif.gz | 194.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yc8.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yc8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7yc8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yc8_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 7yc8_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/7yc8 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/7yc8 | HTTPS FTP |
-Related structure data
Related structure data | 33736MC 7ycgC 7ychC 7yciC 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: 127011.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena (eukaryote) Production host: in vitro transcription vector pT7-Fluc(deltai) (others) References: GenBank: 10832 |
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#2: Chemical | ChemComp-GTP / |
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: Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicing Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.13 MDa / Experimental value: YES |
Source (natural) | Organism: Tetrahymena (eukaryote) |
Source (recombinant) | Organism: in vitro transcription vector pT7-Fluc(deltai) (others) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
Particle selection | Num. of particles selected: 3668247 | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29397 / Symmetry type: POINT |