6SDG

Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with High Affinity DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design principles of a minimal auxin response system.

Kato, H.Mutte, S.K.Suzuki, H.Crespo, I.Das, S.Radoeva, T.Fontana, M.Yoshitake, Y.Hainiwa, E.van den Berg, W.Lindhoud, S.Ishizaki, K.Hohlbein, J.Borst, J.W.Boer, D.R.Nishihama, R.Kohchi, T.Weijers, D.

(2020) Nat Plants 6: 473-482

  • DOI: 10.1038/s41477-020-0662-y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity 1-3 . Gene duplications in families encoding auxin response components have generated tremendous comp ...

    Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity 1-3 . Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development 1,3,4 . However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. The expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned or prevented. This fundamental design probably represents the ancestral system and formed the basis for inflated, complex systems.


    Related Citations: 
    • Design principles of a minimal auxin response system
      Kato, H., Mutte, S.K., Suzuki, H., Crespo, I., Das, S., Radoeva, T., Fontana, M., Yoshitake, Y., Hainiwa, E., van den Berg, W., Lindhoud, S., Hohlbein, J., Borst, J.W., Boer, D.R., Nishihama, R., Kohchi, T., Ishizak, K., Weijers, D.
      (2020) Nat Plants --: --

    Organizational Affiliation

    Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands. dolf.weijers@wur.nl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Auxin response factor
A, B
366Marchantia polymorphaMutation(s): 0 
Gene Names: MpARF2
Find proteins for A0A0K2QVG1 (Marchantia polymorpha)
Go to UniProtKB:  A0A0K2QVG1

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
21-7_AC21Arabidopsis thaliana

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
21-7_BD21Arabidopsis thaliana
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.768α = 90
b = 79.36β = 116.929
c = 79.767γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references