7QD4

Cryo-EM structure of Tn4430 TnpA transposase from Tn3 family in complex with 100 bp long transposon end DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insight into Tn3 family transposition mechanism.

Shkumatov, A.V.Aryanpour, N.Oger, C.A.Goossens, G.Hallet, B.F.Efremov, R.G.

(2022) Nat Commun 13: 6155-6155

  • DOI: https://doi.org/10.1038/s41467-022-33871-z
  • Primary Citation of Related Structures:  
    7QD4, 7QD5, 7QD6, 7QD8

  • PubMed 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 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.


  • Organizational Affiliation

    Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transposase for transposon Tn4430A,
F [auth D]
1,014Bacillus thuringiensisMutation(s): 8 
Gene Names: tnpA
UniProt
Find proteins for P10021 (Bacillus thuringiensis)
Explore P10021 
Go to UniProtKB:  P10021
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10021
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
IR100 DNA substrate, none transferred strandB,
D [auth E]
100Bacillus thuringiensis
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
IR100 DNA substrate, transferred strandC,
E [auth F]
100Bacillus thuringiensis
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.0
MODEL REFINEMENTPHENIX1.19.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)G0H5916N
Research Foundation - Flanders (FWO)G054617N
Fonds National de la Recherche Scientifique (FRNS)BelgiumJ.0162.16
Fonds National de la Recherche Scientifique (FRNS)BelgiumJ.0096.20

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Data collection