7KBE
Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)
Summary for 7KBE
| Entry DOI | 10.2210/pdb7kbe/pdb |
| EMDB information | 22790 22791 |
| Descriptor | Histone H3.2, Histone H4, Histone H2A, ... (6 entities in total) |
| Functional Keywords | nucleosome, m phase, cell cycle, chromatin, xenopus egg extract, dna binding protein, dna binding protein-dna complex, dna binding protein/dna |
| Biological source | Xenopus laevis (African clawed frog) More |
| Total number of polymer chains | 10 |
| Total formula weight | 207621.30 |
| Authors | Arimura, Y.,Funabiki, H. (deposition date: 2020-10-02, release date: 2021-09-15, Last modification date: 2024-05-29) |
| Primary citation | Arimura, Y.,Shih, R.M.,Froom, R.,Funabiki, H. Structural features of nucleosomes in interphase and metaphase chromosomes. Mol.Cell, 81:4377-, 2021 Cited by PubMed Abstract: Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes. PubMed: 34478647DOI: 10.1016/j.molcel.2021.08.010 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.5 Å) |
Structure validation
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