9IU7 | pdb_00009iu7

Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the intermediate-strand exchange state 2

• PDB DOI: https://doi.org/10.2210/pdb9IU7/pdb
• EM Map EMD-60892: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium phage Bxb1, Mycolicibacterium smegmatis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-07-20 Released: 2026-03-04 
• Deposition Author(s): Soma, T., Hiraizumi, M., Yamashita, K., Nishimasu, H.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the intermediate-strand exchange state 2

Soma, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 286.2 kDa 
• Atom Count: 19,472 
• Modeled Residue Count: 2,140 
• Deposited Residue Count: 2,196 
• Unique protein chains: 1
• Unique nucleic acid chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B, C, D	500	Mycobacterium phage Bxb1	Mutation(s): 0  Gene Names: 35, PBI_BXB1_35
UniProt
Find proteins for Q9B086 (Mycobacterium phage Bxb1) Explore Q9B086  Go to UniProtKB:  Q9B086

Entity ID: 2
Molecule	Chains	Length	Organism	Image
attP-L	E [auth E1]	27	Mycobacterium phage Bxb1

Entity ID: 3
Molecule	Chains	Length	Organism	Image
attP-R	F [auth E2]	25	Mycobacterium phage Bxb1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
attP-L	G [auth F1]	25	Mycobacterium phage Bxb1

Entity ID: 5
Molecule	Chains	Length	Organism	Image
attP-R	H [auth F2]	27	Mycobacterium phage Bxb1

Entity ID: 6
Molecule	Chains	Length	Organism	Image
attB-L	I [auth G1]	24	Mycolicibacterium smegmatis

Entity ID: 7
Molecule	Chains	Length	Organism	Image
attB-R	J [auth G2]	22	Mycolicibacterium smegmatis

Entity ID: 8
Molecule	Chains	Length	Organism	Image
attB-L	K [auth H1]	22	Mycolicibacterium smegmatis

Entity ID: 9
Molecule	Chains	Length	Organism	Image
attB-R	L [auth H2]	24	Mycolicibacterium smegmatis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	M [auth A], N [auth B], O [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.08 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: 2026-03-04 
Deposition Author(s): Soma, T., Hiraizumi, M., Yamashita, K., Nishimasu, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAX232F
Japan Science and Technology	Japan	JPMJCR23B6

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release