|Entry||Database: PDB / ID: 7uin|
|Title||CryoEM Structure of an Group II Intron Retroelement|
|Keywords||RNA BINDING PROTEIN/RNA/DNA / RNA / intron / group II / maturase / splicing / retrotransposition / RNA BINDING PROTEIN-RNA-DNA complex|
|Function / homology|
Function and homology information
RNA-directed DNA polymerase / RNA-directed DNA polymerase activity
Similarity search - Function
Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
AMMONIUM ION / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Group II intron reverse transcriptase/maturase
Similarity search - Component
|Biological species||[Eubacterium] rectale (bacteria)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å|
|Authors||Chung, K. / Xu, L.|
|Funding support|| United States, 1items |
|Citation||Journal: Science / Year: 2022|
Title: Structures of a mobile intron retroelement poised to attack its structured DNA target.
Authors: Kevin Chung / Ling Xu / Pengxin Chai / Junhui Peng / Swapnil C Devarkar / Anna Marie Pyle /
Abstract: Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam ...Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam the genome, integrating by reversal of forward splicing. Here we show that retrotransposition is achieved by a tertiary complex between a structurally elaborate ribozyme, its protein mobility factor, and a structured DNA substrate. We solved cryo-electron microscopy structures of an intact group IIC intron-maturase retroelement that was poised for integration into a DNA stem-loop motif. By visualizing the RNP before and after DNA targeting, we show that it is primed for attack and fits perfectly with its DNA target. This study reveals design principles of a prototypical retroelement and reinforces the hypothesis that group II introns are ancient elements of genetic diversification.
|Structure viewer||Molecule: |
Downloads & links
B: E.r IIC Intron
D: Group II intron reverse transcriptase/maturase
A: DNA (37-MER)
-RNA chain / Protein / DNA chain , 3 types, 3 molecules B
|#1: RNA chain|| |
Mass: 206779.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) [Eubacterium] rectale (bacteria)
|#2: Protein|| |
Mass: 49083.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Eubacterium] rectale (bacteria) / Gene: ltrA_2, ltrA, ERS852417_00966, FYL37_05080 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A173ZME3, RNA-directed DNA polymerase
|#3: DNA chain|| |
Mass: 11403.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) [Eubacterium] rectale (bacteria)
-Non-polymers , 3 types, 54 molecules
Mass: 24.305 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N / Feature type: SUBJECT OF INVESTIGATION
|#6: Water|| ChemComp-HOH / |
|Has ligand of interest||Y|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Ternary complex of RNA, protein and DNA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT|
|Molecular weight||Value: 0.260 MDa / Experimental value: NO|
|Source (natural)||Organism: [Eubacterium] rectale (bacteria)|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm|
|Specimen holder||Cryogen: NITROGEN|
|Image recording||Electron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 914099 / Symmetry type: POINT|
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