Human centromere protein B (CENP-B) is a centromere-specific, autoantibody DNA-binding protein that binds to the CENP-B box, which has a 17 bp sequence, and appears in every other alpha-satellite repeat in centromeres and their associated proteins. It has been found to be essential for the formation of minichromosomes.
There are two regions where the CENP-B binds to the CENP-B box are two helix-turn-helix domains and are bound to the major grooves of the DNA. At these locations, kinks are formed, creating a kink-straight-kink bend. The larger, 43° kink is formed due to the unique ‘phosphate bridging by an arginine-rich helix, while the smaller 16° kink is formed by Van der Waals interactions and hydrogen bonds. The overall bend of the CENP-B box is 59°, and may play a role in the structure of centromere-specific chromatin.
It was transparent in PyMOL, but not on Sketchfab and I asked about it but got no response, so pretend the CENP-B box DNA and ribbons on CENP-B are transparent.
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