9UD0 | pdb_00009ud0

Cryo-EM structure of R2Tg bound to template RNA and target DNA in the target-primed reverse transcription initiation state (state 1, Myb domain focused)

• PDB DOI: https://doi.org/10.2210/pdb9UD0/pdb
• NAKB: 9UD0
• EM Map EMD-64057: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Taeniopygia guttata
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-04-06 Released: 2026-10-14 
• Deposition Author(s): Komatsu, D., Hiraizumi, M., Fujimatsu, K., Yamada, S., Yamashita, K., Nishimasu, H.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural mechanism of programmable gene integration by the R2 retrotransposon coupled with CRISPR-Cas9.

Komatsu, D., Hiraizumi, M., Fell, C.W., Fujimatsu, K., Nagahata, N., Yamada, S., Sapkota, S., Ramani, H., Arya, B., Shibata, M., Yamashita, K., Gootenberg, J.S., Abudayyeh, O.O., Nishimasu, H.

(2026) Nat Struct Mol Biol 

• PubMed: 42951937 
• DOI: https://doi.org/10.1038/s41594-026-01903-7
• Primary Citation Related Structures: 
  9UCX, 9UCY, 9UCZ, 9UD0, 9UD1


• PubMed Abstract: 
  

  R2 retroelements are non-long-terminal-repeat retrotransposons that primarily insert into 28S ribosomal DNA loci across diverse eukaryotes. R2 elements home to their target sites through target-primed reverse transcription (TPRT), in which the R2 protein recognizes and nicks the target DNA to prime reverse transcription using an R2-encoding RNA as the template. The avian R2 system from Taeniopygia guttata (R2Tg) can insert a payload sequence within an RNA template into 28S ribosomal DNA loci in human cells. Here, we present cryo-electron microscopy structures of the R2Tg-template RNA-target DNA complex in the TPRT initiation state, both alone and bound to a Cas9-guide RNA complex. These structures provide mechanistic insights into R2Tg-mediated TPRT in its natural context and in the programmable gene integration system STITCHR (site-specific target-primed insertion through targeted CRISPR homing of retroelements). Furthermore, we combine these structural insights with computational protein design methods to engineer an enhanced STITCHR system.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, USA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Institute for Frontier Science Initiative, Kanazawa University, Ishikawa, Japan.
WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Ishikawa, Japan.
Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. [e-mail].
Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, USA. [e-mail].
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. [e-mail].
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].
Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. [e-mail].
Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, USA. [e-mail].
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. [e-mail].
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan. [e-mail].
Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. [e-mail].
Inamori Research Institute for Science, Kyoto, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 186.38 kDa 
• Atom Count: 1,517 
• Modeled Residue Count: 116 
• Deposited Residue Count: 1,417 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase-like protein	A	1,287	Taeniopygia guttata	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
28S DNA top strand	B [auth C]	80	Taeniopygia guttata

Entity ID: 3
Molecule	Chains	Length	Organism	Image
28S DNA bottom strand, 3' side	C [auth D]	50	Taeniopygia guttata

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Servalcat

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Komatsu, D., Hiraizumi, M., Fujimatsu, K., Yamada, S., Yamashita, K., Nishimasu, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	--

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release
  
• Version 1.1: 2026-11-11
  Changes: Data collection, Database references