5JRG
Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)
Summary for 5JRG
| Entry DOI | 10.2210/pdb5jrg/pdb |
| Descriptor | Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (9 entities in total) |
| Functional Keywords | histone fold, dna binding, nucleus, chromatin formation, nucleosome, ap-site, dna binding protein-dna complex, dna binding protein/dna |
| Biological source | Homo sapiens (Human) More |
| Cellular location | Nucleus: P68431 P62805 P04908 P06899 |
| Total number of polymer chains | 10 |
| Total formula weight | 202331.97 |
| Authors | Osakabe, A.,Arimura, Y.,Horikoshi, N.,Kurumizaka, H. (deposition date: 2016-05-06, release date: 2017-03-08, Last modification date: 2023-11-08) |
| Primary citation | Osakabe, A.,Arimura, Y.,Matsumoto, S.,Horikoshi, N.,Sugasawa, K.,Kurumizaka, H. Polymorphism of apyrimidinic DNA structures in the nucleosome Sci Rep, 7:41783-41783, 2017 Cited by PubMed Abstract: Huge amounts (>10,000/day) of apurinic/apyrimidinic (AP) sites are produced in genomes, but their structures in chromatin remain undetermined. We determined the crystal structure of the nucleosome containing AP-site analogs at two symmetric sites, which revealed structural polymorphism: one forms an inchworm configuration without an empty space at the AP site, and the other forms a B-form-like structure with an empty space and the orphan base. This unexpected inchworm configuration of the AP site is important to understand the AP DNA repair mechanism, because it may not be recognized by the major AP-binding protein, APE1, during the base excision repair process. PubMed: 28139742DOI: 10.1038/srep41783 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
Download full validation report
