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 5JGC | pdb_00005jgc

Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A, L130A, L179A and I195A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5JGC

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 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.

Macromolecule Content 

  • Total Structure Weight: 24.8 kDa 
  • Atom Count: 1,711 
  • Modeled Residue Count: 199 
  • Deposited Residue Count: 209 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein TPR1209Oryza sativaMutation(s): 4 
Gene Names: TPR1, ASPR2, TPR2, Os01g0254100, LOC_Os01g15020, OsJ_01134, OSNPB_010254100, P0705D01.10-1
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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.516α = 90
b = 57.516β = 90
c = 174.937γ = 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: 2024-03-06
    Changes: Data collection, Database references