4UDE

An oligomerization domain confers pioneer properties to the LEAFY master floral regulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Sam Oligomerization Domain Shapes the Genomic Binding Landscape of the Leafy Transcription Factor

Sayou, C.Nanao, M.H.Jamin, M.Pose, D.Thevenon, E.Gregoire, L.Tichtinsky, G.Denay, G.Ott, F.Peirats Llobet, M.Schmid, M.Dumas, R.Parcy, F.

(2016) Nat.Commun. 7: 11222

  • DOI: 10.1038/ncomms11222

  • PubMed Abstract: 
  • Deciphering the mechanisms directing transcription factors (TFs) to specific genome regions is essential to understand and predict transcriptional regulation. TFs recognize short DNA motifs primarily through their DNA-binding domain. Some TFs also po ...

    Deciphering the mechanisms directing transcription factors (TFs) to specific genome regions is essential to understand and predict transcriptional regulation. TFs recognize short DNA motifs primarily through their DNA-binding domain. Some TFs also possess an oligomerization domain suspected to potentiate DNA binding but for which the genome-wide influence remains poorly understood. Here we focus on the LEAFY transcription factor, a master regulator of flower development in angiosperms. We have determined the crystal structure of its conserved amino-terminal domain, revealing an unanticipated Sterile Alpha Motif oligomerization domain. We show that this domain is essential to LEAFY floral function. Moreover, combined biochemical and genome-wide assays suggest that oligomerization is required for LEAFY to access regions with low-affinity binding sites or closed chromatin. This finding shows that domains that do not directly contact DNA can nevertheless have a profound impact on the DNA binding landscape of a TF.


    Organizational Affiliation

    Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden.,Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.,Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada V5Z 4H4.,Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain.,Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France.,Institut de Biologie Structurale CEA/DRF, CNRS, Université Grenoble Alpes, 71, avenue des Martyrs, 38044 Grenoble, France.,European Molecular Biology Laboratory, 71, avenue des Martyrs, 38042 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GINLFY PROTEIN
A, B
110Ginkgo bilobaMutation(s): 0 
Gene Names: GinLFY
Find proteins for Q9LLY6 (Ginkgo biloba)
Go to UniProtKB:  Q9LLY6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 81.095α = 90.00
b = 81.095β = 90.00
c = 78.493γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references, Structure summary
  • Version 1.2: 2016-05-04
    Type: Database references