Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor 5

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors.

Boer, D.R.Freire-Rios, A.van den Berg, W.A.Saaki, T.Manfield, I.W.Kepinski, S.Lopez-Vidrieo, I.Franco-Zorrilla, J.M.de Vries, S.C.Solano, R.Weijers, D.Coll, M.

(2014) Cell 156: 577-589

  • DOI: https://doi.org/10.1016/j.cell.2013.12.027
  • Primary Citation of Related Structures:  
    4LDU, 4LDV, 4LDW, 4LDX, 4LDY

  • PubMed Abstract: 

    Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.

  • Organizational Affiliation

    Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Auxin response factor 5397Arabidopsis thalianaMutation(s): 0 
Gene Names: ARF5At1g19850F6F9.10IAA24MP
Find proteins for P93024 (Arabidopsis thaliana)
Explore P93024 
Go to UniProtKB:  P93024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93024
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.613α = 90
b = 91.502β = 114.28
c = 77.182γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references