7NB0

Structure of the DNA-binding domain of SEPALLATA 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors.

Lai, X.Vega-Leon, R.Hugouvieux, V.Blanc-Mathieu, R.van der Wal, F.Lucas, J.Silva, C.S.Jourdain, A.Muino, J.M.Nanao, M.H.Immink, R.Kaufmann, K.Parcy, F.Smaczniak, C.Zubieta, C.

(2021) Nat Commun 12: 4760-4760

  • DOI: https://doi.org/10.1038/s41467-021-24978-w
  • Primary Citation of Related Structures:  
    7NB0

  • PubMed Abstract: 

    The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. Here, we demonstrate that DNA binding in both lineages absolutely requires a short amino acid sequence C-terminal to the MADS domain (M domain) called the Intervening domain (I domain) that was previously defined only in type II lineage MADS. Structural elucidation of the MI domains from the floral regulator, SEPALLATA3 (SEP3), shows a conserved fold with the I domain acting to stabilise the M domain. Using the floral organ identity MADS TFs, SEP3, APETALA1 (AP1) and AGAMOUS (AG), domain swapping demonstrate that the I domain alters genome-wide DNA-binding specificity and dimerisation specificity. Introducing AG carrying the I domain of AP1 in the Arabidopsis ap1 mutant resulted in strong complementation and restoration of first and second whorl organs. Taken together, these data demonstrate that the I domain acts as an integral part of the DNA-binding domain and significantly contributes to the functional identity of the MADS TF.


  • Organizational Affiliation

    Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Developmental protein SEPALLATA 3
A, B, C, D
57Arabidopsis thalianaMutation(s): 0 
Gene Names: SEP3AGL9At1g24260F3I6.19
UniProt
Find proteins for O22456 (Arabidopsis thaliana)
Explore O22456 
Go to UniProtKB:  O22456
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO22456
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.404α = 90
b = 67.436β = 90
c = 122.568γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-16-CE92-0023
Grenoble Instruct-ERIC Center (ISBG)France13317

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description