5SZC

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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:  
    5SZC, 5SZB

  • 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

    Center for Epigenomics, Institute of Genomic Medicine, La Jolla, CA, USA. biren@ucsd.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein DPF3A115Homo sapiensMutation(s): 0 
Gene Names: DPF3BAF45CCERD4
Find proteins for Q92784 (Homo sapiens)
Explore Q92784 
Go to UniProtKB:  Q92784
NIH Common Fund Data Resources
PHAROS  Q92784
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3 tail peptideH18Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
HL-PEPTIDE LINKINGC8 H16 N2 O3LYS
MLZ
Query on MLZ
HL-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 43 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/359 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.321α = 90
b = 39.321β = 90
c = 147.571γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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