4J01

Crystal Structure of Fischerella Transcription Factor HetR complexed with 29mer DNA target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.235 

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

Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets.

Kim, Y.Ye, Z.Joachimiak, G.Videau, P.Young, J.Hurd, K.Callahan, S.M.Gornicki, P.Zhao, J.Haselkorn, R.Joachimiak, A.

(2013) Proc Natl Acad Sci U S A 110: E1716-E1723

  • DOI: https://doi.org/10.1073/pnas.1305971110
  • Primary Citation of Related Structures:  
    4IZZ, 4J00, 4J01

  • PubMed Abstract: 

    HetR is an essential regulator of heterocyst development in cyanobacteria. Many mutations in HetR render Anabaena incapable of nitrogen fixation. The protein binds to a DNA palindrome upstream of hetP and other genes. We have determined the crystal structures of HetR complexed with palindromic DNA targets, 21, 23, and 29 bp at 2.50-, 3.00-, and 3.25-Å resolution, respectively. The highest-resolution structure shows fine details of specific protein-DNA interactions. The lower-resolution structures with longer DNA duplexes have similar interaction patterns and show how the flap domains interact with DNA in a sequence nonspecific fashion. Fifteen of 15 protein-DNA contacts predicted on the basis of the structure were confirmed by single amino acid mutations that abolished binding in vitro and complementation in vivo. A striking feature of the structure is the association of glutamate 71 from each subunit of the HetR dimer with three successive cytosines in each arm of the palindromic target, a feature that is conserved among all known heterocyst-forming cyanobacteria sequenced to date.


  • Organizational Affiliation

    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription Factor HetR
A, B, E, F
302Fischerella thermalis PCC 7521Mutation(s): 0 
Gene Names: hetR
UniProt
Find proteins for Q2ACK9 (Fischerella thermalis PCC 7521)
Explore Q2ACK9 
Go to UniProtKB:  Q2ACK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2ACK9
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (29-MER)
C, D, G, H
29Anabaena
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth G]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.157α = 90
b = 182.182β = 91.38
c = 78.366γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIXrefinement
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2013-06-05
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Structure summary
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description