9C0F | pdb_00009c0f

piggyBat transposase protein-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb9C0F/pdb
• EM Map EMD-45082: EMDB EMDataResource
• NAKB: 9C0F

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Myotis lucifugus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-05-25 Released: 2025-01-29 
• Deposition Author(s): Lannes, L., Hickman, A.B., Dyda, F.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Activity of the mammalian DNA transposon piggyBat from Myotis lucifugus is restricted by its own transposon ends.

Hickman, A.B., Lannes, L., Furman, C.M., Hong, C., Franklin, L., Ghirlando, R., Ghosh, A., Luo, W., Konstantinidou, P., Lorenzi, H.A., Grove, A., Haase, A.D., Wilson, M.H., Dyda, F.

(2025) Nat Commun 16: 458-458

• PubMed: 39774116 
• DOI: https://doi.org/10.1038/s41467-024-55784-9
• Primary Citation Related Structures: 
  9C0F


• PubMed Abstract: 
  

  Members of the piggyBac superfamily of DNA transposons are widely distributed in host genomes ranging from insects to mammals. The human genome has retained five piggyBac-derived genes as domesticated elements although they are no longer mobile. Here, we have investigated the transposition properties of piggyBat from Myotis lucifugus, the only known active mammalian DNA transposon, and show that its low activity in human cells is due to subterminal inhibitory DNA sequences. Activity can be dramatically improved by their removal, suggesting the existence of a mechanism for the suppression of transposon activity. The cryo-electron microscopy structure of the piggyBat transposase pre-synaptic complex showed an unexpected mode of DNA binding and recognition using C-terminal domains that are topologically different from those of the piggyBac transposase. Here we show that structure-based rational re-engineering of the transposase through the removal of putative phosphorylation sites and a changed domain organization - in combination with truncated transposon ends - results in a transposition system that is at least 100-fold more active than wild-type piggyBat.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
Structural Motility, UMR 144 CNRS/Curie Institute, PSL Research University, Paris, cedex 05, France.
International Flavors and Fragrances, Wilmington, DE, USA.
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
Department of Veterans Affairs, Nashville, TN, USA.
Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 157.02 kDa 
• Atom Count: 9,507 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,226 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
piggyBat transposase	C, D	578	Myotis lucifugus	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (35-MER)	A	35	Myotis lucifugus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (35-MER)	B	35	Myotis lucifugus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth C], F [auth C], G [auth D], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Lannes, L., Hickman, A.B., Dyda, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release