Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 8-mer -A6B2 

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

Macromolecule Content

• Total Structure Weight: 203880.50 
• Atom Count: 12095 
• Residue Count: 1318 
• Unique protein chains: 5
• Unique nucleic acid chains: 1

5GTC

Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle

• DOI: 10.2210/pdb5GTC/pdb

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens, Human herpesvirus 8 type P (isolate GK18)
• Expression System: Escherichia coli BL21(DE3), Escherichia coli


• Deposited: 2016-08-19 Released: 2017-06-28 
• Deposition Author(s): Arimura, Y., Kato, D., Suto, H., Kurumizaka, H., Kawashima, S.A., Yamatsugu, K., Kanai, M.
• Funding Organization(s): JST-ERATO Kanai Life Science Catalysis Project; MEXT KAKENHI; null 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.267 
• R-Value Work: 0.211 

Literature

Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.

Amamoto, Y., Aoi, Y., Nagashima, N., Suto, H., Yoshidome, D., Arimura, Y., Osakabe, A., Kato, D., Kurumizaka, H., Kawashima, S.A., Yamatsugu, K., Kanai, M.

(2017) J. Am. Chem. Soc. 139: 7568-7576

• PubMed: 28534629 
• DOI: 10.1021/jacs.7b02138


• PubMed Abstract: 
  

Posttranslational modifications (PTMs) of histones play an important role in the complex regulatory mechanisms governing gene transcription, and their dysregulation can cause diseases such as cancer. The lack of methods for site-selectively modifying native chromatin, however, limits our understanding of the functional roles of a specific histone PTM, not as a single mark, but in the intertwined PTM network. Here, we report a synthetic catalyst DMAP-SH (DSH), which activates chemically stable thioesters (including acetyl-CoA) under physiological conditions and transfers various acyl groups to the proximate amino groups. Our data suggest that DSH, conjugated with a nucleosome ligand, such as pyrrole-imidazole-polyamide and LANA (latency-associated nuclear antigen)-peptide, promotes both natural (including acetylation, butyrylation, malonylation, and ubiquitination) and non-natural (azido- and phosphoryl labeling) PTMs on histones in recombinant nucleosomes and/or in native chromatin, at lysine residues close to the DSH moiety. To investigate the validity of our method, we used LANA-DSH to promote histone H2B lysine-120 (K120) acylation, the function of which is largely unknown. H2BK120 acetylation and malonylation modulated higher-order chromatin structures by reducing internucleosomal interactions, and this modulation was further enhanced by histone tail acetylation. This approach, therefore, may have versatile applications for dissecting the regulatory mechanisms underlying chromatin function.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.1	A, E	139	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens) Go to Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Go to UniProtKB:  P68431

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens) Go to Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 Go to UniProtKB:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1-B/E	C, G	133	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens) Go to Gene View: HIST1H2AB HIST1H2AE Go to UniProtKB:  P04908

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B type 1-J	D, H	129	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens) Go to Gene View: HIST1H2BJ Go to UniProtKB:  P06899

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
LANA peptide	K	12	Human herpesvirus 8 type P (isolate GK18)	Mutation(s): 0  Gene Names: LANA1
Find proteins for Q9QR71 (Human herpesvirus 8 type P (isolate GK18)) Go to UniProtKB:  Q9QR71

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (146-MER)	I,J	146	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	E, I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	A, C, E, G	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NH2	K	NON-POLYMER	H2 N		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.267 
• R-Value Work: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 107.225	α = 90.00
b = 109.017	β = 90.00
c = 176.194	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data collection
Aimless	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-08-19 
• Released Date: 2017-06-28 
• Deposition Author(s): Arimura, Y., Kato, D., Suto, H., Kurumizaka, H., Kawashima, S.A., Yamatsugu, K., Kanai, M.

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Funding Organization	Location	Grant Number
JST-ERATO Kanai Life Science Catalysis Project	Japan	122968
MEXT KAKENHI	Japan	25116002
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Revision History 

• Version 1.0: 2017-06-28
  Type: Initial release