9TEN | pdb_00009ten

PhiC31 excisive synapse: B-bound subregion

• PDB DOI: https://doi.org/10.2210/pdb9TEN/pdb
• EM Map EMD-55830: EMDB EMDataResource
• NAKB: 9TEN

• Classification: RECOMBINATION
• Organism(s): Lomovskayavirus C31
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-11-25 Released: 2026-02-11 
• Deposition Author(s): Sun, Y.E., Spagnolo, L.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.11 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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 137.36 kDa 
• Atom Count: 5,906 
• Modeled Residue Count: 662 
• Deposited Residue Count: 1,018 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombination directionality factor	C [auth J]	271	Lomovskayavirus C31	Mutation(s): 0  Gene Names: 3, rdf
UniProt
Find proteins for Q9T216 (Streptomyces phage phiC31) Explore Q9T216  Go to UniProtKB:  Q9T216

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	D [auth B]	627	Lomovskayavirus C31	Mutation(s): 1  Gene Names: int
UniProt
Find proteins for Q9T221 (Streptomyces phage phiC31) Explore Q9T221  Go to UniProtKB:  Q9T221

Entity ID: 1
Molecule	Chains	Length	Organism	Image
attL60_Fw	A [auth E]	60	Lomovskayavirus C31

Entity ID: 2
Molecule	Chains	Length	Organism	Image
attL60_Rv	B [auth F]	60	Lomovskayavirus C31

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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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