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Yorodumi- PDB-7uim: CryoEM Structure of an Group II Intron Retroelement (apo-complex) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uim | ||||||
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Title | CryoEM Structure of an Group II Intron Retroelement (apo-complex) | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA / intron / group II / maturase / splicing / retrotransposition / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | [Eubacterium] rectale (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Chung, K. / Xu, L. | ||||||
Funding support | United States, 1items
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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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uim.cif.gz | 344.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uim.ent.gz | 256.8 KB | Display | PDB format |
PDBx/mmJSON format | 7uim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uim_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7uim_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7uim_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 7uim_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/7uim ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7uim | HTTPS FTP |
-Related structure data
Related structure data | 26549MC 7uinC 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: 206779.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) [Eubacterium] rectale (bacteria) | ||||
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#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: Chemical | ChemComp-MG / #4: Chemical | 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: Complex of RNA and protein / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.250 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
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: 2500 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 434467 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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