5SZB

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with acetylated K14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of H3K4me1-associated proteins at mammalian enhancers.

Local, A.Huang, H.Albuquerque, C.P.Singh, N.Lee, A.Y.Wang, W.Wang, C.Hsia, J.E.Shiau, A.K.Ge, K.Corbett, K.D.Wang, D.Zhou, H.Ren, B.

(2018) Nat. Genet. 50: 73-82

  • DOI: 10.1038/s41588-017-0015-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enhancers act to regulate cell-type-specific gene expression by facilitating the transcription of target genes. In mammalian cells, active or primed enhancers are commonly marked by monomethylation of histone H3 at lysine 4 (H3K4me1) in a cell-type-s ...

    Enhancers act to regulate cell-type-specific gene expression by facilitating the transcription of target genes. In mammalian cells, active or primed enhancers are commonly marked by monomethylation of histone H3 at lysine 4 (H3K4me1) in a cell-type-specific manner. Whether and how this histone modification regulates enhancer-dependent transcription programs in mammals is unclear. In this study, we conducted SILAC mass spectrometry experiments with mononucleosomes and identified multiple H3K4me1-associated proteins, including many involved in chromatin remodeling. We demonstrate that H3K4me1 augments association of the chromatin-remodeling complex BAF to enhancers in vivo and that, in vitro, H3K4me1-marked nucleosomes are more efficiently remodeled by the BAF complex. Crystal structures of the BAF component BAF45C indicate that monomethylation, but not trimethylation, is accommodated by BAF45C's H3K4-binding site. Our results suggest that H3K4me1 has an active role at enhancers by facilitating binding of the BAF complex and possibly other chromatin regulators.


    Organizational Affiliation

    Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.,National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA.,Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA. biren@ucsd.edu.,Ludwig Institute for Cancer Research, La Jolla, CA, USA. biren@ucsd.edu.,Center for Epigenomics, Institute of Genomic Medicine, La Jolla, CA, USA. biren@ucsd.edu.,Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Aptose Biosciences, Inc., San Diego, CA, USA.,Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger protein DPF3
A
115Homo sapiensMutation(s): 0 
Gene Names: DPF3 (BAF45C, CERD4)
Find proteins for Q92784 (Homo sapiens)
Go to Gene View: DPF3
Go to UniProtKB:  Q92784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3 tail peptide
H
18Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
H
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 39.321α = 90.00
b = 39.321β = 90.00
c = 147.571γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references, Structure summary