6T79

Structure of a human nucleosome at 3.2 A resolution

Summary for 6T79

• Entry DOI: 10.2210/pdb6t79/pdb
• Related: 6T78 6T7A 6T7B 6T7C 6T7D
• EMDB information: 10390
• Descriptor: Histone H3.2, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: nucleosome, dna, histones, nuclear protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 10
• Total formula weight: 205549.03

Authors

Dodonova, S.O.,Zhu, F.,Dienemann, C.,Taipale, J.,Cramer, P. (deposition date: 2019-10-21, release date: 2020-04-29, Last modification date: 2024-05-22)

Primary citation

Dodonova, S.O.,Zhu, F.,Dienemann, C.,Taipale, J.,Cramer, P.
Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Nature, 580:669-672, 2020

PubMed Abstract: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.

PubMed: 32350470
DOI: 10.1038/s41586-020-2195-y

Experimental method

ELECTRON MICROSCOPY (3.2 Å)