8CRA | pdb_00008cra

Structure of the keratin-like domain of SEPALLATA3 and AGAMOUS from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.279 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SEPALLATA-driven MADS transcription factor tetramerization is required for inner whorl floral organ development.

Hugouvieux, V.Blanc-Mathieu, R.Janeau, A.Paul, M.Lucas, J.Xu, X.Ye, H.Lai, X.Le Hir, S.Guillotin, A.Galien, A.Yan, W.Nanao, M.Kaufmann, K.Parcy, F.Zubieta, C.

(2024) Plant Cell 36: 3435-3450

  • DOI: https://doi.org/10.1093/plcell/koae151
  • Primary Citation of Related Structures:  
    8CRA

  • PubMed Abstract: 

    MADS transcription factors are master regulators of plant reproduction and flower development. The SEPALLATA (SEP) subfamily of MADS transcription factors is required for the development of floral organs and plays roles in inflorescence architecture and development of the floral meristem. SEPALLATAs act as organizers of MADS complexes, forming both heterodimers and heterotetramers in vitro. To date, the MADS complexes characterized in angiosperm floral organ development contain at least 1 SEPALLATA protein. Whether DNA binding by SEPALLATA-containing dimeric MADS complexes is sufficient for launching floral organ identity programs, however, is not clear as only defects in floral meristem determinacy were observed in tetramerization-impaired SEPALLATA mutant proteins. Here, we used a combination of genome-wide-binding studies, high-resolution structural studies of the SEP3/AGAMOUS (AG) tetramerization domain, structure-based mutagenesis and complementation experiments in Arabidopsis (Arabidopsis thaliana) sep1 sep2 sep3 and sep1 sep2 sep3 ag-4 plants transformed with versions of SEP3 encoding tetramerization mutants. We demonstrate that while SEP3 heterodimers can bind DNA both in vitro and in vivo and recognize the majority of SEP3 wild-type-binding sites genome-wide, tetramerization is required not only for floral meristem determinacy but also for floral organ identity in the second, third, and fourth whorls.


  • Organizational Affiliation
    • Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Floral homeotic protein AGAMOUS
A, B, C, D
96Arabidopsis thalianaMutation(s): 0 
Gene Names: AGAt4g18960F13C5.130
UniProt
Find proteins for P17839 (Arabidopsis thaliana)
Explore P17839 
Go to UniProtKB:  P17839
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17839
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Developmental protein SEPALLATA 3
E, F, G, H
98Arabidopsis 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: 2.40 Å
  • R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.335α = 90
b = 138.372β = 90
c = 180.229γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Database references, Structure summary