SNAP output for PDB entry 5f99 [SNAP web server]

PDB-id

5f99; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein

Method

X-ray (2.63 Å)

Summary

X-ray structure of the mmtv-a nucleosome core particle

Reference

Frouws TD, Duda SC, Richmond TJ (2016): "X-ray structure of the MMTV-A nucleosome core." Proc.Natl.Acad.Sci.USA, 113, 1214-1219. doi: 10.1073/pnas.1524607113.

Abstract

The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for two similar α-satellite sequences and a sequence (601) selected in vitro have been visualized bound in the nucleosome core. Here we report the 2.6-Å resolution X-ray structure of a nucleosome core particle containing the DNA sequence of nucleosome A of the 3'-LTR of the mouse mammary tumor virus (147 bp MMTV-A). To our knowledge, this is the first nucleosome core particle structure containing a promoter sequence and crystallized from Mg(2+) ions. It reveals sequence-dependent DNA conformations not seen previously, including kinking into the DNA major groove.