5B24

The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer

Horikoshi, N.Tachiwana, H.Kagawa, W.Osakabe, A.Matsumoto, S.Iwai, S.Sugasawa, K.Kurumizaka, H.

(2016) Biochem Biophys Res Commun 471: 117-122

  • DOI: 10.1016/j.bbrc.2016.01.170
  • Primary Citation of Related Structures:  
    5B24

  • PubMed Abstract: 
  • The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the m ...

    The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the mechanism by which the CPD is accommodated within the nucleosome has remained unknown. We now report the crystal structure of a nucleosome containing CPDs. In the nucleosome, the CPD induces only limited local backbone distortion, and the affected bases are accommodated within the duplex. Interestingly, one of the affected thymine bases is located within 3.0 Å from the undamaged complementary adenine base, suggesting the formation of complementary hydrogen bonds in the nucleosome. We also found that UV-DDB, which binds the CPD at the initial stage of the NER pathway, also efficiently binds to the nucleosomal CPD. These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin.


    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; Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address: kurumizaka@waseda.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1 AE139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 BF106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
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PHAROS:  P62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/E CG133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
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PHAROS:  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-J DH129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
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PHAROS:  P06899
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I, J145Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.848α = 90
b = 108.868β = 90
c = 174.053γ = 90
Software Package:
Software NamePurpose
BSSdata collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (MEXT)Japan25116002
Ministry of Education, Culture, Sports, Science and Technology (MEXT)Japan26116521
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations