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Open data
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Basic information
Entry | Database: PDB / ID: 7d0f | |||||||||
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Title | cryo-EM structure of a pre-catalytic group II intron RNP | |||||||||
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![]() | TRANSFERASE/RNA / catalytic RNA / RNA-protein interactions / group II intron / TRANSFERASE-RNA complex | |||||||||
Function / homology | ![]() intron homing / mRNA processing / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å | |||||||||
![]() | Liu, N. / Dong, X.L. / Hu, C.X. / Zeng, J.W. / Wang, J.W. / Wang, J. / Wang, H.W. / Belfort, M. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing. Authors: Nan Liu / Xiaolong Dong / Cuixia Hu / Jianwei Zeng / Jiawei Wang / Jia Wang / Hong-Wei Wang / Marlene Belfort / ![]() ![]() Abstract: Group II introns are the putative progenitors of nuclear spliceosomal introns and use the same two-step splicing pathway. In the cell, the intron RNA forms a ribonucleoprotein (RNP) complex with the ...Group II introns are the putative progenitors of nuclear spliceosomal introns and use the same two-step splicing pathway. In the cell, the intron RNA forms a ribonucleoprotein (RNP) complex with the intron-encoded protein (IEP), which is essential for splicing. Although structures of spliced group II intron RNAs and RNP complexes have been characterized, structural insights into the splicing process remain enigmatic due to lack of pre-catalytic structural models. Here, we report two cryo-EM structures of endogenously produced group II intron RNPs trapped in their pre-catalytic state. Comparison of the catalytically activated precursor RNP to its previously reported spliced counterpart allowed identification of key structural rearrangements accompanying splicing, including a remodeled active site and engagement of the exons. Importantly, altered RNA-protein interactions were observed upon splicing among the RNP complexes. Furthermore, analysis of the catalytically inert precursor RNP demonstrated the structural impact of the formation of the active site on RNP architecture. Taken together, our results not only fill a gap in understanding the structural basis of IEP-assisted group II intron splicing, but also provide parallels to evolutionarily related spliceosomal splicing. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 443.2 KB | Display | ![]() |
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PDB format | ![]() | 338 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 725.8 KB | Display | ![]() |
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Full document | ![]() | 960.1 KB | Display | |
Data in XML | ![]() | 62.7 KB | Display | |
Data in CIF | ![]() | 97.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30532MC ![]() 7d0gC ![]() 7d1aC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: RNA chain | Mass: 295453.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: LtrB Production host: ![]() Strain (production host): IL1403 |
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#2: Protein | Mass: 70286.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ltrA, matR Production host: ![]() Strain (production host): IL1403 References: UniProt: P0A3U0, RNA-directed DNA polymerase, Hydrolases; Acting on ester bonds |
-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
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285.15 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: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203373 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 5G2X Accession code: 5G2X / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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