+Open data
-Basic information
Entry | Database: PDB / ID: 6p5a | |||||||||
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Title | Drosophila P element transposase strand transfer complex | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / transposase / Strand Transfer Complex / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information P-element binding / transposase activity / DNA transposition / DNA integration / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Kellogg, E.H. / Nogales, E. / Ghanim, G. / Rio, D.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structure of a P element transposase-DNA complex reveals unusual DNA structures and GTP-DNA contacts. Authors: George E Ghanim / Elizabeth H Kellogg / Eva Nogales / Donald C Rio / Abstract: P element transposase catalyzes the mobility of P element DNA transposons within the Drosophila genome. P element transposase exhibits several unique properties, including the requirement for a ...P element transposase catalyzes the mobility of P element DNA transposons within the Drosophila genome. P element transposase exhibits several unique properties, including the requirement for a guanosine triphosphate cofactor and the generation of long staggered DNA breaks during transposition. To gain insights into these features, we determined the atomic structure of the Drosophila P element transposase strand transfer complex using cryo-EM. The structure of this post-transposition nucleoprotein complex reveals that the terminal single-stranded transposon DNA adopts unusual A-form and distorted B-form helical geometries that are stabilized by extensive protein-DNA interactions. Additionally, we infer that the bound guanosine triphosphate cofactor interacts with the terminal base of the transposon DNA, apparently to position the P element DNA for catalysis. Our structure provides the first view of the P element transposase superfamily, offers new insights into P element transposition and implies a transposition pathway fundamentally distinct from other cut-and-paste DNA transposases. | |||||||||
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 | 6p5a.cif.gz | 282.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p5a.ent.gz | 216.7 KB | Display | PDB format |
PDBx/mmJSON format | 6p5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p5a_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6p5a_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6p5a_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 6p5a_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/6p5a ftp://data.pdbj.org/pub/pdb/validation_reports/p5/6p5a | HTTPS FTP |
-Related structure data
Related structure data | 20254MC 6pe2C 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
-Transposable element P ... , 2 types, 4 molecules AGBH
#1: Protein | Mass: 65525.992 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-569) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q7M3K2, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Protein | Mass: 16086.797 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 613-747) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q7M3K2, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-DNA chain , 3 types, 6 molecules CIDJEK
#3: DNA chain | Mass: 4827.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) #4: DNA chain | Mass: 11704.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) #5: DNA chain | Mass: 24400.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) |
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-Non-polymers , 2 types, 6 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / |
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-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: Ternary complex of P element transposase in complex with strand transfer DNA Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Drosophila melanogaster (fruit fly) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: UltrAuFoil | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: 4 microliters of concentrated STC complex was applied to a Quantifoil 1.2/1.3 UltraAuFoil grid. After a 30 second incubation, the sample was blotted using blot force of 8 pN and a blot time of 6 seconds. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA / Details: Dataset collected at 40 degree tilt. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1857 |
Image scans | Width: 7420 / Height: 7676 / Movie frames/image: 39 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 253209 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 100 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient |