5JA5

Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A and L130A mutant in complex with rice D53 repressor EAR peptide motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1126/sciadv.1601217
  • Primary Citation of Related Structures:  
    5J9K, 5JA5, 5JGC, 5JHP

  • 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-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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein TPR1209Oryza sativaMutation(s): 2 
Gene Names: TPR1ASPR2TPR2Os01g0254100LOC_Os01g15020OsJ_01134OSNPB_010254100P0705D01.10-1
UniProt
Find proteins for Q5NBT9 (Oryza sativa subsp. japonica)
Explore Q5NBT9 
Go to UniProtKB:  Q5NBT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NBT9
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
The rice D53 peptide (a.a. 794-808)15Oryza sativaMutation(s): 0 
UniProt
Find proteins for Q2RBP2 (Oryza sativa subsp. japonica)
Explore Q2RBP2 
Go to UniProtKB:  Q2RBP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RBP2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.317α = 90
b = 57.317β = 90
c = 173.483γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK071662
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM104212

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description