Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 14-mer - A4B4C3D3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 14-mer - A11B3 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

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

Macromolecule Content

• Total Structure Weight: 350.04 kDa 
• Atom Count: 20244 
• Modelled Residue Count: 1771 
• Deposited Residue Count: 2266 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

5GSE

Crystal structure of unusual nucleosome

• PDB DOI: 10.2210/pdb5GSE/pdb
• NDB: 5GSE

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


• Deposited: 2016-08-16 Released: 2017-05-03 
• Deposition Author(s): Kato, D., Osakabe, A., Arimura, Y., Park, S.Y., Kurumizaka, H.
• Funding Organization(s): MEXT KAKENHI Grant, Agency for Medical Research and Development, the Platform Project for Supporting Drug Discovery and Life Science Research, the Waseda Research Institute for Science and Engineering, Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.255 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

Kato, D., Osakabe, A., Arimura, Y., Mizukami, Y., Horikoshi, N., Saikusa, K., Akashi, S., Nishimura, Y., Park, S.Y., Nogami, J., Maehara, K., Ohkawa, Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama, M., Kurumizaka, H.

(2017) Science 356: 205-208

• PubMed: 28408607 
• DOI: 10.1126/science.aak9867
• Primary Citation of Related Structures:  
  5GSE


• PubMed Abstract: 
  

Nucleosomes are dynamic entities that are repositioned along DNA by chromatin remodeling processes. A nucleosome repositioned by the switch-sucrose nonfermentable (SWI/SNF) remodeler collides with a neighbor and forms the intermediate "overlapping dinucleosome." Here, we report the crystal structure of the overlapping dinucleosome, in which two nucleosomes are associated, at 3.14-angstrom resolution. In the overlapping dinucleosome structure, the unusual "hexasome" nucleosome, composed of the histone hexamer lacking one H2A-H2B dimer from the conventional histone octamer, contacts the canonical "octasome" nucleosome, and they intimately associate. Consequently, about 250 base pairs of DNA are left-handedly wrapped in three turns, without a linker DNA segment between the hexasome and octasome moieties. The overlapping dinucleosome structure may provide important information to understand how nucleosome repositioning occurs during the chromatin remodeling process.

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Organizational Affiliation: 

Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E, K, O	139	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H3A, H3C1, H3FA, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
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, L, P	106	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4C1, H4/A, H4FA, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
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, M	133	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, H2AC4, H2AFM, H2AC8, H2AFA, HIST1H2AE
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, N	129	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ, H2BC11, H2BFR
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 (250-MER)	I	250	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (250-MER)	J	250	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.255 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.582	α = 119.3
b = 101.804	β = 106.51
c = 102.427	γ = 91.36

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-08-16 
• Released Date: 2017-05-03 
Deposition Author(s): Kato, D., Osakabe, A., Arimura, Y., Park, S.Y., Kurumizaka, H.

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Funding Organization	Location	Grant Number
MEXT KAKENHI Grant	Japan	25116002
Agency for Medical Research and Development, the Platform Project for Supporting Drug Discovery and Life Science Research	Japan	--
the Waseda Research Institute for Science and Engineering	Japan	--
Japan Society for the Promotion of Science	Japan	15H06691
Japan Society for the Promotion of Science	Japan	16J06850

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release