9WHY | pdb_00009why

Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the post-strand exchange state

• PDB DOI: https://doi.org/10.2210/pdb9WHY/pdb
• NAKB: 9WHY
• EM Map EMD-65979: EMDB EMDataResource

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


• Deposited: 2025-08-27 Released: 2026-08-12 
• Deposition Author(s): Hiraizumi, M., Tsujimoto, E., Shiojiri, N., Nagahata, N., Yamashita, K., Nishimasu, H.
• Funding Organization(s): Japan Science and Technology, Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural mechanism governing the directionality of bridge recombination.

Hiraizumi, M., Athukoralage, J.S., Perry, N.T., Tsujimoto, E., Shiojiri, N., Nagahata, N., Lee, L., Sun, G., Durrant, M.G., Chandrasekaran, S.S., Konermann, S., Yamashita, K., Hsu, P.D., Nishimasu, H.

(2026) Nature 

• PubMed: 42587149 
• DOI: https://doi.org/10.1038/s41586-026-10903-y
• Primary Citation Related Structures: 
  9WHX, 9WHY


• PubMed Abstract: 
  

  Bridge recombinases from the IS110 family of transposons, such as IS621, associate with a bridge RNA (bRNA) to mediate programmable recombination between donor DNA and target DNA ^1,2 . Although insertion is mediated by the recombinase-bRNA complex, it remains unknown how IS621 elements are excised from host genomes to form the circular DNA intermediates required for transposition. Here we show that bRNA is weakly expressed from IS621 loci in the Escherichia coli genome and that the IS621 recombinase-bRNA complex mediates excision less efficiently than insertion. Furthermore, we present the cryo-electron microscopy structures of the IS621 recombinase-bRNA complex bound to excision DNA substrates, providing mechanistic insights into the excision reaction. Similar to the previously reported donor- and target-bound insertion complex ² , the excision complex comprises two recombinase dimers, each accommodating the target- and donor-binding loops of the bRNA. However, DNA recognition differs notably between the two complexes. Although the donor and target DNAs form a bent U-shape during insertion ² , the excision substrates adopt linear conformations and bind across both bRNA loops, forming an X-shaped structure. This geometry reduces the efficiency of top-strand exchange and contributes to the naturally observed bias favouring insertion over excision. Despite these differences, the efficiencies of both reactions are similarly modulated by base pairing between specific dinucleotides in the bRNA, termed handshake guides, and the top strands of the DNA substrates. Overall, this study provides mechanistic insights into the complete IS110 transposition cycle and facilitates the optimal design of programmable bridge-editing applications.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
Arc Institute, Palo Alto, CA, USA.
Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA.
Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
Arc Institute, Palo Alto, CA, USA. [e-mail].
Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Center for Computational Biology, University of California, Berkeley, Berkeley, CA, 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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 312.79 kDa 
• Atom Count: 14,860 
• Modeled Residue Count: 1,489 
• Deposited Residue Count: 1,836 
• Unique protein chains: 1
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IS621 transposase	A, B, C, D	328	Escherichia coli	Mutation(s): 0  Gene Names: O3K_03330, O3K_03970, O3K_05990, O3K_07835, O3K_09380, O3K_16710, O3K_17245, O3K_20600, O3K_22425
UniProt
Find proteins for A0A0E0Y1P1 (Escherichia coli O104:H4 (strain 2011C-3493)) Explore A0A0E0Y1P1  Go to UniProtKB:  A0A0E0Y1P1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
bridge RNA	E, F	180	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism	Image
LH/RH, top strand	G	49	Escherichia coli

Entity ID: 4
Molecule	Chains	Length	Organism	Image
LH, bottom strand	H	38	Escherichia coli

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RH/LH, top strand	I	33	Escherichia coli

Entity ID: 6
Molecule	Chains	Length	Organism	Image
RH, bottom strand	J	44	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	K [auth A], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Hiraizumi, M., Tsujimoto, E., Shiojiri, N., Nagahata, N., Yamashita, K., Nishimasu, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR23B6
Other private		Inamori Foundation

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release
  
• Version 1.1: 2026-08-26
  Changes: Data collection, Database references