Crystal structure of construct containing A. aeolicus NtrC1 receiver, central and DNA binding domains

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Structure, function, and tethering of DNA-binding domains in sigma (54) transcriptional activators.

Vidangos, N.Maris, A.E.Young, A.Hong, E.Pelton, J.G.Batchelor, J.D.Wemmer, D.E.

(2013) Biopolymers 99: 1082-1096

  • DOI: https://doi.org/10.1002/bip.22333
  • Primary Citation of Related Structures:  
    2M8G, 4L4U, 4L5E

  • PubMed Abstract: 

    We compare the structure, activity, and linkage of DNA-binding domains (DBDs) from σ(54) transcriptional activators and discuss how the properties of the DBDs and the linker to the neighboring domain are affected by the overall properties and requirements of the full proteins. These transcriptional activators bind upstream of specific promoters that utilize σ(54)-polymerase. Upon receiving a signal the activators assemble into hexamers, which then, through adenosine triphosphate (ATP) hydrolysis, drive a conformational change in polymerase that enables transcription initiation. We present structures of the DBDs of activators nitrogen regulatory protein C 1 (NtrC1) and Nif-like homolog 2 (Nlh2) from the thermophile Aquifex aeolicus. The structures of these domains and their relationship to other parts of the activators are discussed. These structures are compared with previously determined structures of the DBDs of NtrC4, NtrC, ZraR, and factor for inversion stimulation. The N-terminal linkers that connect the DBDs to the central domains in NtrC1 and Nlh2 were studied and found to be unstructured. Additionally, a crystal structure of full-length NtrC1 was solved, but density of the DBDs was extremely weak, further indicating that the linker between ATPase and DBDs functions as a flexible tether. Flexible linking of ATPase and DBDs is likely necessary to allow assembly of the active hexameric ATPase ring. The comparison of this set of activators also shows clearly that strong dimerization of the DBD only occurs when other domains do not dimerize strongly.

  • Organizational Affiliation

    Department of Chemistry and QB3 Institute, University of California, Berkeley, CA, 94720-1460.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator (NtrC family)447Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: ntrC1aq_1117
Find proteins for O67198 (Aquifex aeolicus (strain VF5))
Explore O67198 
Go to UniProtKB:  O67198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67198
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.421α = 90
b = 107.01β = 90
c = 98.181γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references