5ZNR

Crystal structure of PtSHL in complex with an H3K27me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL.

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

(2018) Nat Commun 9: 2425-2425

  • DOI: 10.1038/s41467-018-04836-y
  • Primary Citation of Related Structures:  
    5ZNP, 5ZNR

  • PubMed Abstract: 
  • The ability of a cell to dynamically switch its chromatin between different functional states constitutes a key mechanism regulating gene expression. Histone mark "readers" display distinct binding specificity to different histone modifications and play critical roles in regulating chromatin states ...

    The ability of a cell to dynamically switch its chromatin between different functional states constitutes a key mechanism regulating gene expression. Histone mark "readers" display distinct binding specificity to different histone modifications and play critical roles in regulating chromatin states. Here, we show a plant-specific histone reader SHORT LIFE (SHL) capable of recognizing both H3K27me3 and H3K4me3 via its bromo-adjacent homology (BAH) and plant homeodomain (PHD) domains, respectively. Detailed biochemical and structural studies suggest a binding mechanism that is mutually exclusive for either H3K4me3 or H3K27me3. Furthermore, we show a genome-wide co-localization of SHL with H3K27me3 and H3K4me3, and that BAH-H3K27me3 and PHD-H3K4me3 interactions are important for SHL-mediated floral repression. Together, our study establishes BAH-PHD cassette as a dual histone methyl-lysine binding module that is distinct from others in recognizing both active and repressive histone marks.


    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, 201602, China. jmdu@sibs.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SHORT LIFE family proteinA, C [auth B]216Populus trichocarpaMutation(s): 0 
Gene Names: POPTR_0004s16700gPOPTR_004G159900v3POPTR_004G159900
UniProt
Find proteins for B9H0V2 (Populus trichocarpa)
Explore B9H0V2 
Go to UniProtKB:  B9H0V2
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
17-mer peptide from Histone H3.2B [auth P], D [auth Q]17Arabidopsis thalianaMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P59226 (Arabidopsis thaliana)
Explore P59226 
Go to UniProtKB:  P59226
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B [auth P], D [auth Q]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.717α = 90
b = 110.315β = 96.64
c = 58.643γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-10 
  • Released Date: 2018-07-18 
  • Deposition Author(s): Lv, X., Du, J.

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release