9D5L | pdb_00009d5l

The C-terminal domain of Thiopseudomonas alkaliphila Tn7 TnsE bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures.

Krishnan, S.S.Shen, Y.O'Hagan, T.B.Matthews, L.A.Weerasinghe, N.W.Ghirlando, R.Thibodeaux, C.J.Guarne, A.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf472
  • Primary Citation of Related Structures:  
    9D5L

  • PubMed Abstract: 

    Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial chromosome has been extensively studied, the pathway targeting DNA replication structures remains poorly understood. We have used an integrative structural biology approach to elucidate how the Tn7-encoded protein TnsE recognizes replication sites. Using native mass spectrometry, we found that TnsE forms 1:1 and 2:1 (TnsE:DNA) complexes on 3'-recessed DNA, with gain-of-function TnsE variants favoring the formation of 2:1 complexes. Structural characterization confirms that two TnsE molecules bind to DNA with the C-terminal domain of the protein recognizing duplex DNA, leaving the N-terminal domain to impose DNA substrate specificity and recruit the core transposition machinery. Collectively, our work is consistent with a model where TnsE-mediated target-site selection relies on the formation of an asymmetric TnsE:DNA complex to recruit the Tn7 transposase to DNA replication structures.


  • Organizational Affiliation
    • Department of Biochemistry, McGill University, Montreal, QC H3G 0B1, Canada.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TnsE, Tn7 transposition protein166Thiopseudomonas alkaliphilaMutation(s): 0 
UniProt
Find proteins for A0AAW7DSP3 (Thiopseudomonas alkaliphila)
Explore A0AAW7DSP3 
Go to UniProtKB:  A0AAW7DSP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAW7DSP3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNAB [auth C]12synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.77α = 90
b = 63.77β = 90
c = 220.51γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-155941
Canadian Institutes of Health Research (CIHR)CanadaPJT-189946

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release