Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 

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

Macromolecule Content

• Total Structure Weight: 201.75 kDa 
• Atom Count: 11910 
• Modelled Residue Count: 1040 
• Deposited Residue Count: 1304 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

5CPK

Nucleosome containing methylated Sat2L DNA

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

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

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 Biol 5

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


• 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.

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Organizational Affiliation: 

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].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	139	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ, H3C1, H3C2, H3C3, H3FC HIST1H3C, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	133	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908 GTEx:  ENSG00000277075 ENSG00000278463

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	129	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ, H2BFR, H2BC11
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899 GTEx:  ENSG00000124635

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.197	α = 90
b = 109.297	β = 90
c = 173.686	γ = 90

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.

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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
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Derived calculations