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Yorodumi- PDB-7qd6: Cryo-EM structure of Tn4430 TnpA transposase from Tn3 family in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qd6 | |||||||||||||||
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Title | Cryo-EM structure of Tn4430 TnpA transposase from Tn3 family in complex with strand-transfer like DNA product | |||||||||||||||
Components |
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Keywords | RECOMBINATION / DNA transposition / Tn3 family / antibiotic resistance / protein metamorphosis | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Bacillus thuringiensis (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 | 7qd6.cif.gz | 433.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qd6.ent.gz | 333.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qd6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7qd6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7qd6_validation.xml.gz | 67.9 KB | Display | |
Data in CIF | 7qd6_validation.cif.gz | 102.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/7qd6 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/7qd6 | HTTPS FTP |
-Related structure data
Related structure data | 13909MC 7qd4C 7qd5C 7qd8C 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: 116992.117 Da / Num. of mol.: 2 / Mutation: S911R 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 #2: DNA chain | Mass: 21858.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus thuringiensis (bacteria) #3: DNA chain | Mass: 24127.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus thuringiensis (bacteria) #4: DNA chain | Mass: 7105.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus thuringiensis (bacteria) |
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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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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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 / Humidity: 90 % |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 400 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Average exposure time: 3 sec. / Electron dose: 62 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4155 |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / 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: 884091 / Details: cryoSPARC blob picker | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139519 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 167.8 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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