5YE4

Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment

• PDB DOI: https://doi.org/10.2210/pdb5YE4/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2017-09-15 Released: 2018-08-22 
• Deposition Author(s): Matsuda, T., Ito, T., Wakamori, M., Umehara, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.

Handoko, L., Kaczkowski, B., Hon, C.C., Lizio, M., Wakamori, M., Matsuda, T., Ito, T., Jeyamohan, P., Sato, Y., Sakamoto, K., Yokoyama, S., Kimura, H., Minoda, A., Umehara, T.

(2018) Epigenetics 13: 410-431

• PubMed: 30080437 
• DOI: https://doi.org/10.1080/15592294.2018.1469891
• Primary Citation of Related Structures:  
  5YE3, 5YE4


• PubMed Abstract: 
  

  The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found that a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and -independent manner.

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Organizational Affiliation: 

a Division of Genomic Technologies , RIKEN Center for Life Science Technologies, Yokohama , Kanagawa , Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.83 kDa 
• Atom Count: 7,414 
• Modelled Residue Count: 860 
• Deposited Residue Count: 872 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1A9D7 VH CH1 chain	A, C	211	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1A9D7 L chain	B, D	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
di-acetylated histone H4	E, F	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth C], V [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	E, F	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.346	α = 90
b = 164.093	β = 104.5
c = 73.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Matsuda, T., Ito, T., Wakamori, M., Umehara, T.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description