Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 350035.91 
• Atom Count: 20244 
• Residue Count: 2266 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

5GSE

Crystal structure of unusual nucleosome

• 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


• 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 

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


• 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: 

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, K, O	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, L, P	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, M	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, N	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: 5
Molecule	Chains	Length	Organism
DNA (250-MER)	I	250	synthetic construct

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

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: 3.14 Å
• R-Value Free: 0.255 
• R-Value Work: 0.197 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 90.582	α = 119.30
b = 101.804	β = 106.51
c = 102.427	γ = 91.36

Software Package:

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

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