9I86 | pdb_00009i86

Enterobacteriaphage PRD1 - P12 protein filament in complex with poly(dT) ssDNA

• PDB DOI: https://doi.org/10.2210/pdb9I86/pdb
• NAKB: 9I86
• EM Map EMD-52710: EMDB EMDataResource
• EM Map EMD-52708: EMDB EMDataResource
• EM Map EMD-52709: EMDB EMDataResource

• Classification: REPLICATION
• Organism(s): Enterobacteria phage PRD1, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-04 Released: 2025-03-19 
• Deposition Author(s): Degen, M., Traeger, K.L., Hiller, S.
• Funding Organization(s): Swiss Nanoscience Institute

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12.

Trager, L.K., Degen, M., Pereira, J., Durairaj, J., Teixeira, R.D., Hiller, S., Huguenin-Dezot, N.

(2025) Nucleic Acids Res 53

• PubMed: 40052821 
• DOI: https://doi.org/10.1093/nar/gkaf132
• Primary Citation Related Structures: 
  9GFQ, 9I86


• PubMed Abstract: 
  

  Protein-primed DNA replication is a unique mechanism, bioorthogonal to other known DNA replication modes. It relies on specialised single-stranded DNA (ssDNA)-binding proteins (SSBs) to stabilise ssDNA intermediates by unknown mechanisms. Here, we present the structural and biochemical characterisation of P12, an SSB from bacteriophage PRD1. High-resolution cryo-electron microscopy reveals that P12 forms a unique, cooperative filament along ssDNA. Each protomer binds the phosphate backbone of 6 nucleotides in a sequence-independent manner, protecting ssDNA from nuclease degradation. Filament formation is driven by an intrinsically disordered C-terminal tail, facilitating cooperative binding. We identify residues essential for ssDNA interaction and link the ssDNA-binding ability of P12 to toxicity in host cells. Bioinformatic analyses place the P12 fold as a distinct branch within the OB-like fold family. This work offers new insights into protein-primed DNA replication and lays a foundation for biotechnological applications.

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Organizational Affiliation: 
• Department of Biosystems Science and Engineering, ETH Zurich, Schanzenstrasse 44, 4056 Basel, Switzerland.
Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland.
SIB Swiss Institute of Bioinformatics, University of Basel, Elisabethenstrasse 43, 4051 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 148.61 kDa 
• Atom Count: 6,890 
• Modeled Residue Count: 850 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, D [auth B], E [auth C], F [auth D], G [auth E], H [auth F]	160	Enterobacteria phage PRD1	Mutation(s): 0  Gene Names: XII
UniProt
Find proteins for P17637 (Enterobacteria phage PRD1) Explore P17637  Go to UniProtKB:  P17637

Entity ID: 2
Molecule	Chains	Length	Organism	Image
ssDNA poly(dT), 80mer	B [auth Y], C [auth Z]	80	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Degen, M., Traeger, K.L., Hiller, S.

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Funding Organization	Location	Grant Number
Swiss Nanoscience Institute	Switzerland	--

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release