6KMJ

Crystal structure of Sth1 bromodomain in complex with H3K14Ac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Literature

The Structural Basis for Specific Recognition of H3K14 Acetylation by Sth1 in the RSC Chromatin Remodeling Complex.

Chen, G.Li, W.Yan, F.Wang, D.Chen, Y.

(2020) Structure 28: 111

  • DOI: 10.1016/j.str.2019.10.015
  • Primary Citation of Related Structures:  
    6KMJ, 6KMB

  • PubMed Abstract: 
  • The Saccharomyces cerevisiae RSC (Remodel the Structure of Chromatin) complex is a chromatin-remodeling complex and plays essential roles in transcription regulation and DNA repair. The acetylation of H3 Lysine14 (H3K14Ac) enhances the RSC retention on nucleosomes and increases the remodeling activity of RSC ...

    The Saccharomyces cerevisiae RSC (Remodel the Structure of Chromatin) complex is a chromatin-remodeling complex and plays essential roles in transcription regulation and DNA repair. The acetylation of H3 Lysine14 (H3K14Ac) enhances the RSC retention on nucleosomes and increases the remodeling activity of RSC. However, which RSC component recognizes H3K14Ac remains unclear. Here, we discovered that the bromodomain of the catalytic subunit Sth1 (Sth1 BD ) possessed the strongest affinity to H3K14Ac among all RSC bromodomains. The Sth1 BD specifically recognized the K(Ac)ΦΦR motif (Φ stands for any hydrophobic amino acid), including H3K14Ac and H4K20Ac. We determined the crystal structures of Sth1 BD at 2.40 Å resolution and Sth1 BD -H3K14Ac complex at 1.40 Å resolution. The extensive interfaces between Sth1 BD and H3 6-21 facilitate the specific and robust binding of Sth1 BD to H3K14Ac. Our studies provide insights into how the RSC complex recognizes H3K14Ac to orchestrate the crosstalk between histone acetylation and chromatin remodeling.


    Organizational Affiliation

    State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, P. R. China. Electronic address: yongchen@sibcb.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear protein STH1/NPS1 A112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STH1NPS1YIL126W
EC: 3.6.4.12
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32597 
Go to UniProtKB:  P32597
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3 C17Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHT1YBR010WYBR0201HHT2SIN2YNL031CN2749
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P61830 
Go to UniProtKB:  P61830
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
CL-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.943α = 90
b = 61.933β = 90
c = 153.151γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670748

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references