9IBL | pdb_00009ibl

PhiC31 integrative synapse: attB x attP with an S12A integrase variant

• PDB DOI: https://doi.org/10.2210/pdb9IBL/pdb
• EM Map EMD-52811: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Lomovskayavirus C31
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-12 Released: 2026-02-11 
• Deposition Author(s): Spagnolo, L., Sun, Y.E., Joseph, A.P.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural mechanisms of unidirectional prophage integration and excision by serine integrases

Sun, Y.E., Aspinall, L., Joseph, A.P., Colloms, S.D., Stark, W.M., Spagnolo, L.

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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 347.5 kDa 
• Atom Count: 18,811 
• Modeled Residue Count: 2,058 
• Deposited Residue Count: 2,726 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A [auth B], B [auth A], C, D	625	Lomovskayavirus C31	Mutation(s): 0  Gene Names: int
UniProt
Find proteins for Q9T221 (Streptomyces phage phiC31) Explore Q9T221  Go to UniProtKB:  Q9T221

Entity ID: 2
Molecule	Chains	Length	Organism	Image
attP_Rv	E [auth F]	60	Lomovskayavirus C31

Entity ID: 3
Molecule	Chains	Length	Organism	Image
attP_Fw	F [auth E]	60	Lomovskayavirus C31

Entity ID: 4
Molecule	Chains	Length	Organism	Image
attB_Fw	G	53	Lomovskayavirus C31

Entity ID: 5
Molecule	Chains	Length	Organism	Image
attB_Rv	H	53	Lomovskayavirus C31

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Spagnolo, L., Sun, Y.E., Joseph, A.P.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/W017571/1

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release