5J9K

Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) in complex with rice D53 repressor EAR peptide motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex.

Ma, H.Duan, J.Ke, J.He, Y.Gu, X.Xu, T.H.Yu, H.Wang, Y.Brunzelle, J.S.Jiang, Y.Rothbart, S.B.Xu, H.E.Li, J.Melcher, K.

(2017) Sci Adv 3: e1601217-e1601217

  • DOI: 10.1126/sciadv.1601217
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • TOPLESS are tetrameric plant corepressors of the conserved Tup1/Groucho/TLE (transducin-like enhancer of split) family. We show that they interact through their TOPLESS domains (TPDs) with two functionally important ethylene response factor-associate ...

    TOPLESS are tetrameric plant corepressors of the conserved Tup1/Groucho/TLE (transducin-like enhancer of split) family. We show that they interact through their TOPLESS domains (TPDs) with two functionally important ethylene response factor-associated amphiphilic repression (EAR) motifs of the rice strigolactone signaling repressor D53: the universally conserved EAR-3 and the monocot-specific EAR-2. We present the crystal structure of the monocot-specific EAR-2 peptide in complex with the TOPLESS-related protein 2 (TPR2) TPD, in which the EAR-2 motif binds the same TPD groove as jasmonate and auxin signaling repressors but makes additional contacts with a second TPD site to mediate TPD tetramer-tetramer interaction. We validated the functional relevance of the two TPD binding sites in reporter gene assays and in transgenic rice and demonstrate that EAR-2 binding induces TPD oligomerization. Moreover, we demonstrate that the TPD directly binds nucleosomes and the tails of histones H3 and H4. Higher-order assembly of TPD complexes induced by EAR-2 binding markedly stabilizes the nucleosome-TPD interaction. These results establish a new TPD-repressor binding mode that promotes TPD oligomerization and TPD-nucleosome interaction, thus illustrating the initial assembly of a repressor-corepressor-nucleosome complex.


    Related Citations: 
    • Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors.
      Ke, J.,Ma, H.,Gu, X.,Thelen, A.,Brunzelle, J.S.,Li, J.,Xu, H.E.,Melcher, K.
      (2015) Sci Adv 1: e1500107


    Organizational Affiliation

    Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein TPR1
A, B
209Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: TPR1 (ASPR2, TPR2)
Find proteins for Q5NBT9 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q5NBT9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
rice D53 peptide 794-808
C, D
15Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: D53
Find proteins for Q2RBP2 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q2RBP2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.718α = 90.00
b = 59.638β = 90.00
c = 171.183γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK071662
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM102545
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM104212

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence