5ZNP

Crystal structure of PtSHL in complex with an H3K4me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.249 

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:  

  • 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 p ...

    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

    Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA. xuehua.zhong@wisc.edu.,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.,Morgridge Institute for Research, Madison, WI, 53706, USA.,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.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA. xuehua.zhong@wisc.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SHORT LIFE family protein
A, B
216Populus trichocarpaMutation(s): 0 
Find proteins for B9H0V2 (Populus trichocarpa)
Go to UniProtKB:  B9H0V2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
15-mer peptide from Histone H3.2
P, Q
15Arabidopsis thalianaMutation(s): 0 
Gene Names: HTR2, HTR3, HTR13, HTR9, HTR1
Find proteins for P59226 (Arabidopsis thaliana)
Go to UniProtKB:  P59226
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
P, Q
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.340α = 90.00
b = 91.909β = 90.00
c = 114.370γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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