5B73

Crystal structure of human ZMYND8 PHD-Bromo-PWWP domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report



Literature

ZMYND8 Reads the Dual Histone Mark H3K4me1-H3K14ac to Antagonize the Expression of Metastasis-Linked Genes

Li, N.Li, Y.Lv, J.Zheng, X.Wen, H.Shen, H.Zhu, G.Chen, T.Y.Dhar, S.S.Kan, P.Y.Wang, Z.Shiekhattar, R.Shi, X.Lan, F.Chen, K.Li, W.Li, H.Lee, M.G.

(2016) Mol Cell 63: 470-484

  • DOI: 10.1016/j.molcel.2016.06.035
  • Primary Citation of Related Structures:  
    5B73

  • PubMed Abstract: 
  • Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating fun ...

    Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating functions of H3K14ac and H3K4me1, we here show that the dual histone modification mark H3K4me1-H3K14ac is recognized by ZMYND8 (also called RACK7) and can function to counteract gene expression. We identified ZMYND8 as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 antagonized the expression of metastasis-linked genes, and its knockdown increased the cellular invasiveness in vitro and in vivo. The plant homeodomain (PHD) and Bromodomain cassette in ZMYND8 mediated the combinatorial recognition of H3K4me1-H3K14ac and H3K4me0-H3K14ac by ZMYND8. These findings uncover an unexpected role for the signature H3K4me1-H3K14ac in attenuating gene expression and reveal a metastasis-suppressive epigenetic mechanism in which ZMYND8's PHD-Bromo cassette couples H3K4me1-H3K14ac with downregulation of metastasis-linked genes.


    Organizational Affiliation

    Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA. Electronic address: mglee@mdanderson.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein kinase C-binding protein 1A339Homo sapiensMutation(s): 0 
Gene Names: ZMYND8KIAA1125PRKCBP1RACK7
Find proteins for Q9ULU4 (Homo sapiens)
Explore Q9ULU4 
Go to UniProtKB:  Q9ULU4
NIH Common Fund Data Resources
PHAROS  Q9ULU4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.083α = 90
b = 67.999β = 90
c = 70.309γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-06-03 
  • Released Date: 2016-11-02 
  • Deposition Author(s): Li, H., Li, Y., Zheng, X.

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release