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 1.1 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: 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 ...

    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

    Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA. xuehua.zhong@wisc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H3K4me2 peptideB [auth P],
D [auth Q],
F [auth R]
15Arabidopsis thalianaMutation(s): 0 
Gene Names: 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B [auth P],
D [auth Q],
F [auth R]
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
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

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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