8XJV
Structural basis for the linker histone H5-nucleosome binding and chromatin compaction
This is a non-PDB format compatible entry.
Summary for 8XJV
| Entry DOI | 10.2210/pdb8xjv/pdb |
| EMDB information | 37637 37638 38407 |
| Descriptor | DNA, Histone H2A, Histone H2B 1.1, ... (7 entities in total) |
| Functional Keywords | chromatin fiber, histone, dna, linker histone, nucleosome, epigenetics, genome folding, interaction, gene regulation |
| Biological source | synthetic construct More |
| Total number of polymer chains | 110 |
| Total formula weight | 2882027.78 |
| Authors | |
| Primary citation | Li, W.,Hu, J.,Song, F.,Yu, J.,Peng, X.,Zhang, S.,Wang, L.,Hu, M.,Liu, J.C.,Wei, Y.,Xiao, X.,Li, Y.,Li, D.,Wang, H.,Zhou, B.R.,Dai, L.,Mou, Z.,Zhou, M.,Zhang, H.,Zhou, Z.,Zhang, H.,Bai, Y.,Zhou, J.Q.,Li, W.,Li, G.,Zhu, P. Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction. Cell Res., 34:707-724, 2024 Cited by PubMed Abstract: The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo. PubMed: 39103524DOI: 10.1038/s41422-024-01009-z PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.6 Å) |
Structure validation
Download full validation report
