9GFQ | pdb_00009gfq

Structure of PRD1 SSB P12

• PDB DOI: https://doi.org/10.2210/pdb9GFQ/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Enterobacteria phage PRD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-12 Released: 2025-04-09 
• Deposition Author(s): Traeger, L.K., Huguenin-Dezot, N.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.228 (DCC) 

Starting Model: in silico

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.67 kDa 
• Atom Count: 943 
• Modeled Residue Count: 117 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A	160	Enterobacteria phage PRD1	Mutation(s): 0  Gene Names: XII
UniProt
Find proteins for P17637 (Enterobacteria phage PRD1) Explore P17637  Go to UniProtKB:  P17637

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.228 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.434	α = 90
b = 50.999	β = 90
c = 56.344	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Traeger, L.K., Huguenin-Dezot, N.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	PZ00P3_202090

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release
  
• Version 1.1: 2025-04-23
  Changes: Database references