2PNH | pdb_00002pnh

Escherichia coli PriB E39A variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.276 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A hand-off mechanism for primosome assembly in replication restart.

Lopper, M.Boonsombat, R.Sandler, S.J.Keck, J.L.

(2007) Mol Cell 26: 781-793

  • DOI: https://doi.org/10.1016/j.molcel.2007.05.012
  • Primary Citation of Related Structures:  
    2PNH

  • PubMed Abstract: 

    Collapsed DNA replication forks must be reactivated through origin-independent reloading of the replication machinery (replisome) to ensure complete duplication of cellular genomes. In E. coli, the PriA-dependent pathway is the major replication restart mechanism and requires primosome proteins PriA, PriB, and DnaT for replisome reloading. However, the molecular mechanisms that regulate origin-independent replisome loading are not fully understood. Here, we demonstrate that assembly of primosome protein complexes represents a key regulatory mechanism, as inherently weak PriA-PriB and PriB-DnaT interactions are strongly stimulated by single-stranded DNA. Furthermore, the binding site on PriB for single-stranded DNA partially overlaps the binding sites for PriA and DnaT, suggesting a dynamic primosome assembly process in which single-stranded DNA is handed off from one primosome protein to another as a repaired replication fork is reactivated. This model helps explain how origin-independent initiation of DNA replication is restricted to repaired replication forks, preventing overreplication of the genome.


  • Organizational Affiliation
    • Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, 550 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Primosomal replication protein n
A, B
107Escherichia coli K-12Mutation(s): 1 
Gene Names: priB
UniProt
Find proteins for P07013 (Escherichia coli (strain K12))
Explore P07013 
Go to UniProtKB:  P07013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07013
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.978α = 90
b = 60.685β = 90
c = 66.273γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary