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Yorodumi- PDB-7d1a: cryo-EM structure of a group II intron RNP complexed with its rev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d1a | |||||||||
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Title | cryo-EM structure of a group II intron RNP complexed with its reverse transcriptase | |||||||||
Components |
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Keywords | TRANSFERASE/RNA / catalytic RNA / RNA-protein interactions / TRANSFERASE-RNA complex | |||||||||
Function / homology | Function and homology information 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 | Lactococcus lactis subsp. cremoris (lactic acid bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Liu, N. / Dong, X.L. / Hu, C.X. / Zeng, J.W. / Wang, J.W. / Wang, J. / Wang, H.W. / Belfort, M. | |||||||||
Funding support | China, United States, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2020 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. | |||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7d1a.cif.gz | 423.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d1a.ent.gz | 325.5 KB | Display | PDB format |
PDBx/mmJSON format | 7d1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d1a_validation.pdf.gz | 746.9 KB | Display | wwPDB validaton report |
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Full document | 7d1a_full_validation.pdf.gz | 886.8 KB | Display | |
Data in XML | 7d1a_validation.xml.gz | 49.2 KB | Display | |
Data in CIF | 7d1a_validation.cif.gz | 76.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/7d1a ftp://data.pdbj.org/pub/pdb/validation_reports/d1/7d1a | HTTPS FTP |
-Related structure data
Related structure data | 3331M 7d0fC 7d0gC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 70286.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Gene: ltrA, matR Production host: Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain (production host): IL1403 References: UniProt: P0A3U0, RNA-directed DNA polymerase, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 291363.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Production host: Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain (production host): IL1403 |
#3: RNA chain | Mass: 4068.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Production host: Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain (production host): IL1403 |
-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 a group II intron RNP complexed with its reverse transcriptase Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Lactococcus lactis subsp. cremoris (lactic acid bacteria) |
Source (recombinant) | Organism: Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain: IL1403 |
Buffer solution | pH: 8 |
Specimen | 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 | ||||||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 450296 / Symmetry type: POINT | ||||||||||||||||||||||||
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