5B73 | pdb_00005b73

Crystal structure of human ZMYND8 PHD-Bromo-PWWP domain

• PDB DOI: https://doi.org/10.2210/pdb5B73/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

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

• PubMed: 27477906 
• DOI: https://doi.org/10.1016/j.molcel.2016.06.035
• Primary Citation 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 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.

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Organizational Affiliation: 
• Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
Institute for Academic Medicine, The Methodist Hospital Research Institute, Houston, TX 77030, USA; Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, The Methodist Hospital Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
Key Laboratory of Epigenetics, Institutes of Biomedical Sciences and Key Laboratory of Birth Defect, Children's Hospital, Fudan University, Shanghai 201102, China.
Department of Environmental Health Sciences, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205, USA.
University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA.
Division of Biostatistics, Dan L. Duncan Cancer Center, and Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Electronic address: [e-mail].
MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China. Electronic address: [e-mail].
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.26 kDa 
• Atom Count: 2,712 
• Modeled Residue Count: 313 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase C-binding protein 1	A	339	Homo sapiens	Mutation(s): 0  Gene Names: ZMYND8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULU4 (Homo sapiens) Explore Q9ULU4  Go to UniProtKB:  Q9ULU4
PHAROS:  Q9ULU4 GTEx:  ENSG00000101040

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.083	α = 90
b = 67.999	β = 90
c = 70.309	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations