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 1.3 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: https://doi.org/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 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

    Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka-shi, Osaka 560-8531, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
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UniProt GroupP68431
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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Go to UniProtKB:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
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Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER)
I, J
145Homo sapiens
Sequence Annotations
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  • Reference Sequence
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  (Full details and data files)

  • 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
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary