Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 8-mer -A8 

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

Macromolecule Content

• Total Structure Weight: 201750.66 
• Atom Count: 11910 
• Residue Count: 1304 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

5CPK

Nucleosome containing methylated Sat2L DNA

• DOI: 10.2210/pdb5CPK/pdb
• NDB: 5CPK

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli


• Deposited: 2015-07-21 Released: 2015-10-28 
• Deposition Author(s): Osakabe, A., Arimura, Y., Adachi, F., Maehara, K., Ohkawa, Y., Kurumizaka, H.
• Funding Organization(s): MEXT KAKENHI; the Platform for Drug Discovery, Informatics, and Structural Life Science from MEXT; JSPS KAKENHI 

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.632 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 

Literature

Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.

Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H.

(2015) Open Biology 5: --

• PubMed: 26446621 
• DOI: 10.1098/rsob.150128
• Primary Citation of Related Structures:  
  5CPJ, 5CPI


• PubMed Abstract: 
  

DNA methylation occurs on CpG sites and is important to form pericentric heterochromatin domains. The satellite 2 sequence, containing seven CpG sites, is located in the pericentric region of human chromosome 1 and is highly methylated in normal cells. In contrast, the satellite 2 region is reportedly hypomethylated in cancer cells, suggesting that the methylation status may affect the chromatin structure around the pericentric regions in tumours. In this study, we mapped the nucleosome positioning on the satellite 2 sequence in vitro and found that DNA methylation modestly affects the distribution of the nucleosome positioning. The micrococcal nuclease assay revealed that the DNA end flexibility of the nucleosomes changes, depending on the DNA methylation status. However, the structures and thermal stabilities of the nucleosomes are unaffected by DNA methylation. These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells.

---

Organizational Affiliation: 

Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan [e-mail].,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, 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: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens) 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: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens) 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: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens) 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: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens) Go to UniProtKB:  P06899

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (145-MER)	I	145	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism
DNA (145-MER)	J	145	Homo sapiens

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5CM	I, J	DNA LINKING	C10 H16 N3 O7 P		DC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.632 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 105.197	α = 90.00
b = 109.297	β = 90.00
c = 173.686	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-07-21 
• Released Date: 2015-10-28 
• Deposition Author(s): Osakabe, A., Arimura, Y., Adachi, F., Maehara, K., Ohkawa, Y., Kurumizaka, H.

---

Funding Organization	Location	Grant Number
MEXT KAKENHI	Japan	25116002
the Platform for Drug Discovery, Informatics, and Structural Life Science from MEXT	Japan	--
JSPS KAKENHI	Japan	26840025

Revision History 

• Version 1.0: 2015-10-28
  Type: Initial release