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Open data
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Basic information
Entry | Database: PDB / ID: 7xsl | ||||||||||||||||||
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Title | Misfolded Tetrahymena ribozyme conformation 2 | ||||||||||||||||||
![]() | RNA (388-MER) | ||||||||||||||||||
![]() | RNA / Misfolded Tetrahymena Ribozyme / Topological Crossing / Cryo-EM / refolding | ||||||||||||||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å | ||||||||||||||||||
![]() | Li, S. / Palo, M. / Pintilie, G. / Zhang, X. / Su, Z. / Kappel, K. / Chiu, W. / Zhang, K. / Das, R. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Topological crossing in the misfolded ribozyme resolved by cryo-EM. Authors: Shanshan Li / Michael Z Palo / Grigore Pintilie / Xiaojing Zhang / Zhaoming Su / Kalli Kappel / Wah Chiu / Kaiming Zhang / Rhiju Das / ![]() ![]() Abstract: The group I intron has been a key system in the understanding of RNA folding and misfolding. The molecule folds into a long-lived misfolded intermediate (M) , which has been known to form extensive ...The group I intron has been a key system in the understanding of RNA folding and misfolding. The molecule folds into a long-lived misfolded intermediate (M) , which has been known to form extensive native-like secondary and tertiary structures but is separated by an unknown kinetic barrier from the native state (N). Here, we used cryogenic electron microscopy (cryo-EM) to resolve misfolded structures of the L-21 ScaI ribozyme. Maps of three M substates (M1, M2, M3) and one N state were achieved from a single specimen with overall resolutions of 3.5 Å, 3.8 Å, 4.0 Å, and 3.0 Å, respectively. Comparisons of the structures reveal that all the M substates are highly similar to N, except for rotation of a core helix P7 that harbors the ribozyme's guanosine binding site and the crossing of the strands J7/3 and J8/7 that connect P7 to the other elements in the ribozyme core. This topological difference between the M substates and N state explains the failure of 5'-splice site substrate docking in M, supports a topological isomer model for the slow refolding of M to N due to a trapped strand crossing, and suggests pathways for M-to-N refolding. | ||||||||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 270.2 KB | Display | ![]() |
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PDB format | ![]() | 209.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 990.8 KB | Display | ![]() |
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Full document | ![]() | 1003.8 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33426MC ![]() 7xskC ![]() 7xsmC ![]() 7xsnC 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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1 |
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Components
#1: RNA chain | Mass: 125402.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: in vitro transcription vector pT7-TP(deltai) (others) References: GenBank: 10832 |
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-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: Misfolded Tetrahymena ribozyme conformation 2 / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.12 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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: 2800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 51.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 42382 |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 10414332 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 431156 / Symmetry type: POINT |