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Yorodumi- PDB-7qd8: Cryo-EM structure of Tn4430 TnpA transposase from Tn3 family in a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qd8 | |||||||||||||||
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Title | Cryo-EM structure of Tn4430 TnpA transposase from Tn3 family in apo state | |||||||||||||||
Components | Transposase for transposon Tn4430 | |||||||||||||||
Keywords | RECOMBINATION / DNA transposition / Tn3 family / antibiotic resistance / protein metamorphosis | |||||||||||||||
Function / homology | Tn3 transposase DDE domain / Domain of unknown function DUF4158 / : / Tn3 transposase DDE domain / Domain of unknown function (DUF4158) / transposase activity / DNA transposition / DNA binding / Transposase for transposon Tn4430 Function and homology information | |||||||||||||||
Biological species | Bacillus thuringiensis (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Shkumatov, A.V. / Oger, C.A. / Aryanpour, N. / Hallet, B.F. / Efremov, R.G. | |||||||||||||||
Funding support | Belgium, 4items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural insight into Tn3 family transposition mechanism. Authors: Alexander V Shkumatov / Nicolas Aryanpour / Cédric A Oger / Gérôme Goossens / Bernard F Hallet / Rouslan G Efremov / Abstract: Transposons are diverse mobile genetic elements that play the critical role as genome architects in all domains of life. Tn3 is a widespread family and among the first identified bacterial ...Transposons are diverse mobile genetic elements that play the critical role as genome architects in all domains of life. Tn3 is a widespread family and among the first identified bacterial transposons famed for their contribution to the dissemination of antibiotic resistance. Transposition within this family is mediated by a large TnpA transposase, which facilitates both transposition and target immunity. Howtever, a structural framework required for understanding the mechanism of TnpA transposition is lacking. Here, we describe the cryo-EM structures of TnpA from Tn4430 in the apo form and paired with transposon ends before and after DNA cleavage and strand transfer. We show that TnpA has an unusual architecture and exhibits a family specific regulatory mechanism involving metamorphic refolding of the RNase H-like catalytic domain. The TnpA structure, constrained by a double dimerization interface, creates a peculiar topology that suggests a specific role for the target DNA in transpososome assembly and activation. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qd8.cif.gz | 315.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qd8.ent.gz | 252.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qd8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7qd8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7qd8_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 7qd8_validation.cif.gz | 82 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/7qd8 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/7qd8 | HTTPS FTP |
-Related structure data
Related structure data | 13910MC 7qd4C 7qd5C 7qd6C C: citing same article (ref.) M: map data used to model this data |
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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: Protein | Mass: 116922.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: tnpA / Production host: Escherichia coli (E. coli) / References: UniProt: P10021 |
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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: TnpA transposase in apo state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 / Details: 50 mM HEPES (pH 7.5), 100 mM NaCl, 30 mM L-Arg HCL |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
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 / Nominal defocus max: 5300 nm / Nominal defocus min: 600 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Average exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3724 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4751313 / Details: cryoSPARC blob picker | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399477 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 159 / Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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