5ZNR | pdb_00005znr

Crystal structure of PtSHL in complex with an H3K27me3 peptide

• PDB DOI: https://doi.org/10.2210/pdb5ZNR/pdb

• Classification: GENE REGULATION
• Organism(s): Populus trichocarpa, Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-10 Released: 2018-07-18 
• Deposition Author(s): Lv, X., Du, J.
• Funding Organization(s): Ministry of Science and Technology (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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

• PubMed: 29930355 
• DOI: https://doi.org/10.1038/s41467-018-04836-y
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Wisconsin Institute for Discovery, University of Wisconsin-Madison, 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.
Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Morgridge Institute for Research, Madison, WI, 53706, USA.
Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].
Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].
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. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 54.25 kDa 
• Atom Count: 3,165 
• Modeled Residue Count: 391 
• Deposited Residue Count: 466 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHORT LIFE family protein	A, C [auth B]	216	Populus trichocarpa	Mutation(s): 0  Gene Names: POPTR_0004s16700g, POPTR_004G159900v3
UniProt
Find proteins for B9H0V2 (Populus trichocarpa) Explore B9H0V2  Go to UniProtKB:  B9H0V2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
17-mer peptide from Histone H3.2	B [auth P], D [auth Q]	17	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P59226 (Arabidopsis thaliana) Explore P59226  Go to UniProtKB:  P59226

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B [auth P], D [auth Q]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.717	α = 90
b = 110.315	β = 96.64
c = 58.643	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0503200

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description