4OX0

Crystal structure of the keratin-like domain from the MADS transcription factor Sepallata 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for the Oligomerization of the MADS Domain Transcription Factor SEPALLATA3 in Arabidopsis.

Puranik, S.Acajjaoui, S.Conn, S.Costa, L.Conn, V.Vial, A.Marcellin, R.Melzer, R.Brown, E.Hart, D.Theien, G.Silva, C.S.Parcy, F.Dumas, R.Nanao, M.Zubieta, C.

(2014) Plant Cell 26: 3603-3615

  • DOI: 10.1105/tpc.114.127910

  • PubMed Abstract: 
  • In plants, MADS domain transcription factors act as central regulators of diverse developmental pathways. In Arabidopsis thaliana, one of the most central members of this family is SEPALLATA3 (SEP3), which is involved in many aspects of plant reprodu ...

    In plants, MADS domain transcription factors act as central regulators of diverse developmental pathways. In Arabidopsis thaliana, one of the most central members of this family is SEPALLATA3 (SEP3), which is involved in many aspects of plant reproduction, including floral meristem and floral organ development. SEP3 has been shown to form homo and heterooligomeric complexes with other MADS domain transcription factors through its intervening (I) and keratin-like (K) domains. SEP3 function depends on its ability to form specific protein-protein complexes; however, the atomic level determinants of oligomerization are poorly understood. Here, we report the 2.5-Å crystal structure of a small portion of the intervening and the complete keratin-like domain of SEP3. The domains form two amphipathic alpha helices separated by a rigid kink, which prevents intramolecular association and presents separate dimerization and tetramerization interfaces comprising predominantly hydrophobic patches. Mutations to the tetramerization interface demonstrate the importance of highly conserved hydrophobic residues for tetramer stability. Atomic force microscopy was used to show SEP3-DNA interactions and the role of oligomerization in DNA binding and conformation. Based on these data, the oligomerization patterns of the larger family of MADS domain transcription factors can be predicted and manipulated based on the primary sequence.


    Organizational Affiliation

    Department of Genetics, Friedrich Schiller University, 07737 Jena, Germany.,European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France.,CNRS, Laboratoire de Physiologie Cellulaire and Végétale, UMR 5168, 38054 Grenoble, France Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, Laboratoire de Physiologie Cellulaire et Végétale, USC1359, F-38054 Grenoble, France.,Université Grenoble Alpes, CNRS, Integrated Structural Biology Grenoble, Unit of Virus Host Cell Interactions, Unité Mixte Internationale 3265 (CNRS-EMBL-UJF), UMS 3518 (CNRS-CEA-UJF-EMBL), 38042 Grenoble, France.,European Synchrotron Radiation Facility, Structural Biology Group, 38042 Grenoble, France Faculté des Sciences de Montpellier, place Eugène Bataillon, 34095 Montpellier, France.,CNRS, Laboratoire de Physiologie Cellulaire and Végétale, UMR 5168, 38054 Grenoble, France Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, Laboratoire de Physiologie Cellulaire et Végétale, USC1359, F-38054 Grenoble, France chloe.zubieta@cea.fr.,European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France Unit for Virus Host-Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France.,Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide SA 5000, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Developmental protein SEPALLATA 3
A, B, C, D
104Arabidopsis thalianaMutation(s): 0 
Gene Names: SEP3 (AGL9)
Find proteins for O22456 (Arabidopsis thaliana)
Go to UniProtKB:  O22456
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 123.071α = 90.00
b = 143.197β = 90.00
c = 48.287γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
BUSTERrefinement
XSCALEdata scaling
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-01
    Type: Author supporting evidence