9DOU | pdb_00009dou

Taeniopygia guttata R2 retrotransposon (R2Tg) initiating target-primed reverse transcription

• PDB DOI: https://doi.org/10.2210/pdb9DOU/pdb
• NAKB: 9DOU
• EM Map EMD-47091: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA/DNA
• Organism(s): Taeniopygia guttata
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2024-09-19 Released: 2025-05-21 
• Deposition Author(s): Wilkinson, M.E., Edmonds, K.H.K., Zhang, F.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons.

Edmonds, K.K., Wilkinson, M.E., Strebinger, D., Chen, H., Lash, B., Schaefer, C.C., Zhu, S., Liu, D., Zilberzwige-Tal, S., Ladha, A., Walsh, M.L., Frangieh, C.J., Vaz Reay, N.A., Macrae, R.K., Wang, X., Zhang, F.

(2025) Nat Commun 16: 6079-6079

• PubMed: 40603868 
• DOI: https://doi.org/10.1038/s41467-025-61321-z
• Primary Citation of Related Structures:  
  9DOU


• PubMed Abstract: 
  

  R2 elements, a class of non-long terminal repeat (non-LTR) retrotransposons, have the potential to be harnessed for transgene insertion. However, efforts to achieve this are limited by our understanding of the retrotransposon mechanisms. Here, we structurally and biochemically characterize R2 from Taeniopygia guttata (R2Tg). We show that R2Tg cleaves both strands of its ribosomal DNA target and binds a pseudoknotted RNA element within the R2 3' UTR to initiate target-primed reverse transcription. Guided by these insights, we engineer and characterize an all-RNA system for transgene insertion. We substantially reduce the system's size and insertion scars by eliminating unnecessary R2 sequences on the donor. We further improve the integration efficiency by chemically modifying the 5' end of the donor RNA and optimizing delivery, creating a compact system that achieves over 80% integration efficiency in several human cell lines. This work expands the genome engineering toolbox and provides mechanistic insights that will facilitate future development of R2-mediated gene insertion tools.

---

Organizational Affiliation: 
• Howard Hughes Medical Institute, Cambridge, MA, USA.
Yang Tan Collective, Cambridge, MA, USA.
McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Stanley Center for Psychiatric Research, Broad Institute of MIT, Cambridge, MA, 02142, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA. [e-mail].
Yang Tan Collective, Cambridge, MA, USA. [e-mail].
McGovern Institute for Brain Research at MIT, Cambridge, MA, USA. [e-mail].
Broad Institute of MIT and Harvard, Cambridge, MA, USA. [e-mail].
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 398.93 kDa 
• Atom Count: 10,494 
• Modeled Residue Count: 1,069 
• Deposited Residue Count: 2,158 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
R2Tg retrotransposon ORF	A	1,390	Taeniopygia guttata	Mutation(s): 0
UniProt
Find proteins for A0A803VHT8 (Ficedula albicollis) Explore A0A803VHT8  Go to UniProtKB:  A0A803VHT8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
28S DNA bottom strand, 3' side	B	211	Taeniopygia guttata

Entity ID: 3
Molecule	Chains	Length	Organism	Image
28S DNA bottom strand, 5' side (priming strand)	C [auth P]	13	Taeniopygia guttata

Entity ID: 4
Molecule	Chains	Length	Organism	Image
R2Tg 3'UTR RNA	D [auth R]	333	Taeniopygia guttata

Entity ID: 5
Molecule	Chains	Length	Organism	Image
28S DNA top strand	E [auth T]	211	Taeniopygia guttata

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	G [auth A]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
ZN	H [auth A], I [auth A], J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	5.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Wilkinson, M.E., Edmonds, K.H.K., Zhang, F.

---

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2025-07-16
  Changes: Data collection, Database references