4YM6

Crystal structure of the human nucleosome containing 6-4PP (outside)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.514 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome

Osakabe, A.Tachiwana, H.Kagawa, W.Horikoshi, N.Matsumoto, S.Hasegawa, M.Matsumoto, N.Toga, T.Yamamoto, J.Hanaoka, F.Thoma, N.H.Sugasawa, K.Iwai, S.Kurumizaka, H.

(2015) Sci Rep 5: 16330-16330

  • DOI: 10.1038/srep16330
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes 6-4PP lesions through a base flipping mechanism. As genomic DNA is almost entirely accommodated within nucleosomes, the flipping of the 6-4PP bases is supposed to be ...

    UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes 6-4PP lesions through a base flipping mechanism. As genomic DNA is almost entirely accommodated within nucleosomes, the flipping of the 6-4PP bases is supposed to be extremely difficult if the lesion occurs in a nucleosome, especially on the strand directly contacting the histone surface. Here we report that UV-DDB binds efficiently to nucleosomal 6-4PPs that are rotationally positioned on the solvent accessible or occluded surface. We determined the crystal structures of nucleosomes containing 6-4PPs in these rotational positions, and found that the 6-4PP DNA regions were flexibly disordered, especially in the strand exposed to the solvent. This characteristic of 6-4PP may facilitate UV-DDB binding to the damaged nucleosome. We present the first atomic-resolution pictures of the detrimental DNA cross-links of neighboring pyrimidine bases within the nucleosome, and provide the mechanistic framework for lesion recognition by UV-DDB 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
139Homo sapiensGene 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 UniProtKB:  P68431
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Homo sapiensGene 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 UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
C, G
133Homo sapiensGene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens)
Go to Gene View: HIST1H2AB HIST1H2AE
Go to UniProtKB:  P04908
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
129Homo sapiensGene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens)
Go to Gene View: HIST1H2BJ
Go to UniProtKB:  P06899
Entity ID: 5
MoleculeChainsLengthOrganism
145-MER DNAI,J145Homo sapiens
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
T64
Query on T64
I, J
DNA linkingC20 H28 N4 O15 P2DT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.514 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.713α = 90.00
b = 109.483β = 90.00
c = 178.214γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Japan Society for the Promotion of ScienceJapan25250023
Ministry of Education, Culture, Sports, Science and TechnologyJapan25131720
Ministry of Education, Culture, Sports, Science and TechnologyJapan25116002

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release