5GSE

Crystal structure of unusual nucleosome


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 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1126/science.aak9867
  • Structures With Same Primary Citation

  • 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 di ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E, K, O
139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L, P
106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
C, G, M
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AC4H2AFMH2AC8H2AFAHIST1H2AE
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H, N
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BC11H2BFR
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsLengthOrganism
DNA (250-MER)I250synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (250-MER)J250synthetic 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 = 90.582α = 119.3
b = 101.804β = 106.51
c = 102.427γ = 91.36
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXT KAKENHI GrantJapan25116002
Agency for Medical Research and Development, the Platform Project for Supporting Drug Discovery and Life Science ResearchJapan--
the Waseda Research Institute for Science and EngineeringJapan--
Japan Society for the Promotion of ScienceJapan15H06691
Japan Society for the Promotion of ScienceJapan16J06850

Revision History 

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