+Open data
-Basic information
Entry | Database: PDB / ID: 7lcc | ||||||
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Title | Helitron transposase bound to LTS | ||||||
Components |
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Keywords | RECOMBINATION / Helitron / transposase / evolution / gene editing / gene capture / rolling circle / replication / nuclease / helicase / relaxase | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) Myotis lucifugus (little brown bat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å | ||||||
Authors | Kosek, D. / Dyda, F. | ||||||
Funding support | 1items
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Citation | Journal: Mol Cell / Year: 2021 Title: The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end. Authors: Dalibor Kosek / Ivana Grabundzija / Haotian Lei / Ilija Bilic / Huaibin Wang / Yukun Jin / Graham F Peaslee / Alison B Hickman / Fred Dyda / Abstract: Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle ...Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes. Although most eukaryotic transposases form oligomers and use RNase H-like domains to break and rejoin double-stranded DNA (dsDNA), Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain. Here, we report the cryo-electron microscopy structure of a Helitron transposase bound to the 5'-transposon end, providing insight into its multidomain architecture and function. The monomeric transposase forms a tightly packed assembly that buries the covalently attached cleaved end, protecting it until the second end becomes available. The structure reveals unexpected architectural similarity to TraI, a bacterial relaxase that also catalyzes ssDNA movement. The HUH active site suggests how two juxtaposed tyrosines, a feature of many replication initiators that use HUH nucleases, couple the conformational shift of an α-helix to control strand cleavage and ligation reactions. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lcc.cif.gz | 293.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lcc.ent.gz | 229.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lcc_validation.pdf.gz | 726.1 KB | Display | wwPDB validaton report |
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Full document | 7lcc_full_validation.pdf.gz | 736.2 KB | Display | |
Data in XML | 7lcc_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 7lcc_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/7lcc ftp://data.pdbj.org/pub/pdb/validation_reports/lc/7lcc | HTTPS FTP |
-Related structure data
Related structure data | 23271MC 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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1 |
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-Components
#1: Protein | Mass: 171253.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm) |
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#2: DNA chain | Mass: 6158.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Myotis lucifugus (little brown bat) |
#3: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-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: Helraiser complex with LTS / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.17 MDa / Experimental value: YES |
Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 73.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1982458 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 937125 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL Details: The initial model has been traced manualy, then refined in Rosetta and finished in Coot 9.0 |