Aquifex aeolicus replicative helicase (DnaB) complexed with ADP, at 3.3 resolution

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

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Nucleotide and partner-protein control of bacterial replicative helicase structure and function.

Strycharska, M.S.Arias-Palomo, E.Lyubimov, A.Y.Erzberger, J.P.O'Shea, V.L.Bustamante, C.J.Berger, J.M.

(2013) Mol Cell 52: 844-854

  • DOI: https://doi.org/10.1016/j.molcel.2013.11.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cellular replication forks are powered by ring-shaped, hexameric helicases that encircle and unwind DNA. To better understand the molecular mechanisms and control of these enzymes, we used multiple methods to investigate the bacterial replicative helicase, DnaB. A 3.3 Å crystal structure of Aquifex aeolicus DnaB, complexed with nucleotide, reveals a newly discovered conformational state for this motor protein. Electron microscopy and small angle X-ray scattering studies confirm the state seen crystallographically, showing that the DnaB ATPase domains and an associated N-terminal collar transition between two physical states in a nucleotide-dependent manner. Mutant helicases locked in either collar state are active but display different capacities to support critical activities such as duplex translocation and primase-dependent RNA synthesis. Our findings establish the DnaB collar as an autoregulatory hub that controls the ability of the helicase to transition between different functional states in response to both nucleotide and replication initiation/elongation factors.

  • Organizational Affiliation

    Biophysics Program, University of California, Berkeley, Berkeley, CA 94720-3220, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3220, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicative DNA helicase
A, B
434Aquifex aeolicus VF5Mutation(s): 3 
Gene Names: dnaBaq_1472
Find proteins for O67450 (Aquifex aeolicus (strain VF5))
Explore O67450 
Go to UniProtKB:  O67450
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67450
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.707α = 90
b = 195.707β = 90
c = 195.707γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release