5NQS | pdb_00005nqs

Structure of the Arabidopsis Thaliana TOPLESS N-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.247 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression.

Martin-Arevalillo, R.Nanao, M.H.Larrieu, A.Vinos-Poyo, T.Mast, D.Galvan-Ampudia, C.Brunoud, G.Vernoux, T.Dumas, R.Parcy, F.

(2017) Proc Natl Acad Sci U S A 114: 8107-8112

  • DOI: https://doi.org/10.1073/pnas.1703054114
  • Primary Citation Related Structures: 
    5NQS, 5NQV

  • PubMed Abstract: 

    Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as Arabidopsis thaliana , the most prominent corepressor is TOPLESS (TPL), which plays a key role in hormone signaling and development. Here we present the crystallographic structure of the Arabidopsis TPL N-terminal region comprising the LisH and CTLH (C-terminal to LisH) domains and a newly identified third region, which corresponds to a CRA domain. Comparing the structure of TPL with the mammalian TBL1, which shares a similar domain structure and performs a parallel corepressor function, revealed that the plant TPLs have evolved a new tetramerization interface and unique and highly conserved surface for interaction with repressors. Using site-directed mutagenesis, we validated those surfaces in vitro and in vivo and showed that TPL tetramerization and repressor binding are interdependent. Our results illustrate how evolution used a common set of protein domains to create a diversity of corepressors, achieving similar properties with different molecular solutions.


  • Organizational Affiliation
    • Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives/Biosciences and Biotechnology Institute of Grenoble, Institut National de la Recherche Agronomique (INRA), F-38000 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 50.59 kDa 
  • Atom Count: 3,060 
  • Modeled Residue Count: 357 
  • Deposited Residue Count: 420 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein TOPLESS
A, B
210Arabidopsis thalianaMutation(s): 0 
Gene Names: TPLWSIP1At1g15750F7H2.9
UniProt
Find proteins for Q94AI7 (Arabidopsis thaliana)
Explore Q94AI7 
Go to UniProtKB:  Q94AI7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94AI7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.247 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.681α = 90
b = 72.681β = 90
c = 181.147γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description