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

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


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: https://doi.org/10.1038/s41588-017-0015-6
  • Primary Citation of Related Structures:  
    5SZB, 5SZC

  • 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-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

    Ludwig Institute for Cancer Research, La Jolla, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein DPF3115Homo sapiensMutation(s): 0 
Gene Names: DPF3BAF45CCERD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92784 (Homo sapiens)
Explore Q92784 
Go to UniProtKB:  Q92784
PHAROS:  Q92784
GTEx:  ENSG00000205683 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92784
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3 tail peptideB [auth H]18Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.321α = 90
b = 39.321β = 90
c = 147.571γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations