6E83 | pdb_00006e83

Solution structure of ZZZ3 ZZ domain in complex with histone H3 tail

• PDB DOI: https://doi.org/10.2210/pdb6E83/pdb
• BMRB: 30501

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-27 Released: 2018-09-19 
• Deposition Author(s): Zhang, Y., Kutateladze, T.G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation.

Mi, W., Zhang, Y., Lyu, J., Wang, X., Tong, Q., Peng, D., Xue, Y., Tencer, A.H., Wen, H., Li, W., Kutateladze, T.G., Shi, X.

(2018) Nat Commun 9: 3759-3759

• PubMed: 30217978 
• DOI: https://doi.org/10.1038/s41467-018-06247-5
• Primary Citation Related Structures: 
  6E83, 6E86


• PubMed Abstract: 
  

  Recognition of histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Most reader modules target specific post-translational modifications on histones. Here, we report the identification of a reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-two-A-containing (ATAC) histone acetyltransferase complex. The solution NMR structure of the ZZ in complex with the H3 peptide reveals a unique binding mechanism involving caging of the N-terminal Alanine 1 of histone H3 in an acidic cavity of the ZZ domain, indicating a specific recognition of H3 versus other histones. Depletion of ZZZ3 or disruption of the ZZ-H3 interaction dampens ATAC-dependent promoter histone H3K9 acetylation and target gene expression. Overall, our study identifies the ZZ domain of ZZZ3 as a histone H3 reader that is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation.

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Organizational Affiliation: 
• Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA.
Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA.
Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA. [e-mail].
Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA. [e-mail].
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.72 kDa 
• Atom Count: 598 
• Modeled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZZ-type zinc finger-containing protein 3	A [auth B]	64	Homo sapiens	Mutation(s): 0  Gene Names: ZZZ3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYH5 (Homo sapiens) Explore Q8IYH5  Go to UniProtKB:  Q8IYH5
PHAROS:  Q8IYH5 GTEx:  ENSG00000036549

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	B [auth A]	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Zhang, Y., Kutateladze, T.G.

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations