4NMN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report



Literature

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: 10.1016/j.molcel.2013.11.016
  • Primary Citation of Related Structures:  
    4NMN

  • 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 hel ...

    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; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3220, USA. Electronic address: jmberger@jhmi.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicative DNA helicaseAB434Aquifex aeolicus VF5Mutation(s): 3 
Gene Names: dnaBaq_1472
EC: 3.6.4.12
Find proteins for O67450 (Aquifex aeolicus (strain VF5))
Explore O67450 
Go to UniProtKB:  O67450
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SR
Query on SR

Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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