5Z8N

Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.

Yang, Z.Qian, S.Scheid, R.N.Lu, L.Chen, X.Liu, R.Du, X.Lv, X.Boersma, M.D.Scalf, M.Smith, L.M.Denu, J.M.Du, J.Zhong, X.

(2018) Nat Genet 50: 1247-1253

  • DOI: https://doi.org/10.1038/s41588-018-0187-8
  • Primary Citation of Related Structures:  
    5Z8L, 5Z8N

  • PubMed Abstract: 

    The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes 1-5 . In plants, timely transition to a flowering state is crucial for successful reproduction 6-9 . EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis thaliana 10,11 . We found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. We observed co-enrichment of a subset of EBS-associated genes with H3K4me3, H3K27me3, and Polycomb repressor complex 2 (PRC2). Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3. This binding balance was critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induced early floral transition. Our results identify a bivalent chromatin reader capable of recognizing two antagonistic histone marks, and we propose a distinct mechanism of interaction between active and repressive chromatin states.


  • Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin remodeling protein EBSA,
C [auth B],
E [auth C]
199Arabidopsis thalianaMutation(s): 0 
Gene Names: EBSAt4g22140F1N20.240
UniProt
Find proteins for F4JL28 (Arabidopsis thaliana)
Explore F4JL28 
Go to UniProtKB:  F4JL28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4JL28
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H3K4me2 peptideB [auth P],
D [auth Q],
F [auth R]
15Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P59226 (Arabidopsis thaliana)
Explore P59226 
Go to UniProtKB:  P59226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59226
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.464α = 90
b = 75.696β = 115.41
c = 80.357γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0503200

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description