Finished reading this preprint on the ALC1-#nucleosome complex? ⬆️

The methods section details what worked, but not everything that was tried: it would be way too long for the academic article format (this methods section is already quite long).

Well, if you are curious about the thought process and decision making during data analysis, rejoice! For @HRBridges has written it all up in Part 2 of the case study in the CryoSPARC Guide!

Find it here: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-processing-of-a-novel-motor-bound-nucleosome-state-empiar-10739-part-2

Discuss it on the forum here: https://discuss.cryosparc.com/t/case-study-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739-part-2/24438
Or directly here on the Fediverse.

So what does this new structure look like?

ALC1 is loosely bound to the #nucleosome, in a conformation that likely doesn't allow it to slide the nucleosome along the DNA, since the two ATPase lobes are not clamping the DNA. But we finally see the macro domain, for the first time in a nucleosome-bound structure! It interacts with the N-ATPase lobe, preventing the ATPase domain from fully clamping the DNA. So this looks a lot like an intermediate state in the transition from auto-inhibited to active ALC1.

Another striking observation from this structure is a long alpha-helix just upstream of the macro domain, that lines the nucleosome's minor super-groove.

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As promised, here is a summary of this new preprint on the ALC1-nucleosome complex. 🧵

https://doi.org/10.1101/2025.11.10.687450

First, a reminder of some structural features of the #nucleosome.

Histones H2A and H2B form a negatively charged cleft exposed on the surface of the histone octamer, called the "acidic patch". It is recognized by many chromatin-binding factors. If you have read on these proteins, you have most likely already read about the acidic patch too.

One feature much less commonly mentioned is the "super-groove". The DNA wraps around the histone octamer in such a way that the major and minor grooves perfectly align across the two gyres. In 2004, Dervan, Luger and colleagues synthesized short polyamides able to bind to specific sequences across the super-groove (https://doi.org/10.1073/pnas.0401743101). They hypothesized that some chromatin-binding factors may recognize the super-groove, among other nucleosomal epitopes. Until 2025, there was no direct evidence for this.

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