Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Asymmetric fluctuation of overlapping dinucleosome studied by cryoelectron microscopy and small-angle X-ray scattering.
Journal, issue, pages	PNAS Nexus, Vol. 3, Issue 11, Page pgae484, Year 2024
Publish date	Oct 27, 2024
Authors	Masahiro Shimizu / Hiroki Tanaka / Masahiro Nishimura / Nobuhiro Sato / Kayo Nozawa / Haruhiko Ehara / Shun-Ichi Sekine / Ken Morishima / Rintaro Inoue / Yoshimasa Takizawa / Hitoshi Kurumizaka / Masaaki Sugiyama /
PubMed Abstract	Nucleosome remodelers modify the local structure of chromatin to release the region from nucleosome-mediated transcriptional suppression. Overlapping dinucleosomes (OLDNs) are nucleoprotein complexes ...Nucleosome remodelers modify the local structure of chromatin to release the region from nucleosome-mediated transcriptional suppression. Overlapping dinucleosomes (OLDNs) are nucleoprotein complexes formed around transcription start sites as a result of remodeling, and they consist of two nucleosome moieties: a histone octamer wrapped by DNA (octasome) and a histone hexamer wrapped by DNA (hexasome). While OLDN formation alters chromatin accessibility to proteins, the structural mechanism behind this process is poorly understood. Thus, this study investigated the characteristics of structural fluctuations in OLDNs. First, multiple structures of the OLDN were visualized through cryoelectron microscopy (cryoEM), providing an overview of the tilting motion of the hexasome relative to the octasome at the near-atomistic resolution. Second, small-angle X-ray scattering (SAXS) revealed the presence of OLDN conformations with a larger radius of gyration than cryoEM structures. A more complete description of OLDN fluctuation was proposed by SAXS-based ensemble modeling, which included possible transient structures. The ensemble model supported the tilting motion of the OLDN outlined by the cryoEM models, further suggesting the presence of more diverse conformations. The amplitude of the relative tilting motion of the hexasome was larger, and the nanoscale fluctuation in distance between the octasome and hexasome was also proposed. The cryoEM models were found to be mapped in the energetically stable region of the conformational distribution of the ensemble. Exhaustive complex modeling using all conformations that appeared in the structural ensemble suggested that conformational and motional asymmetries of the OLDN result in asymmetries in the accessibility of OLDN-binding proteins.
External links	PNAS Nexus / PubMed:39539301 / PubMed Central
Methods	EM (single particle)
Resolution	4.54 - 5.32 Å
Structure data	38877 8y3c EMDB-38877, PDB-8y3c: Cryo-EM structure of the overlapping di-nucleosome (closed form) Method: EM (single particle) / Resolution: 5.21 Å 38878 8y3d EMDB-38878, PDB-8y3d: Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Method: EM (single particle) / Resolution: 5.1 Å 38879 8y3e EMDB-38879, PDB-8y3e: Cryo-EM structure of the overlapping di-nucleosome (open form) Method: EM (single particle) / Resolution: 5.32 Å 38880 8y3f EMDB-38880, PDB-8y3f: Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Method: EM (single particle) / Resolution: 4.54 Å
Source	homo sapiens (human) synthetic construct (others)
Keywords	GENE REGULATION/DNA / chromatin / GENE REGULATION / GENE REGULATION-DNA complex