Guillaume Gaullier

Now I wait however long it takes to build the entire complex. With the partial model feature, maybe I could have my new, smaller subunits built in 10 minutes instead.

One feature I'd like in such programs is the ability to provide a partial model to save time. Very often we have maps with one thing already well-known and with good models already available, and only need help to model the new additional subunits.

I just moved my account to a personal data server (PDS) hosted in Europe: www.eurosky.tech
The migration tool made it very easy!

So I might use Bluesky a bit more often. Although it is on Mastodon that I really feel at home, as far as social media go (and I will keep the fedi-bridge on for now).

I was skeptical of Bluesky from the start, especially because its decentralized nature didn't seem easily actionable in practice, and because its main (and, for a while, only) personal data server (PDS) is hosted in the US (which inspires less confidence every day, these days...).

Question for the #cryoEM crowd: have you played with ModelAngelo, CryoAtom and EMProt, and would you care to offer thoughts/notes on the comparison? I have ModelAngelo installed and I love it, but the other two claim improved performance - which should I try first?

ChimeraX screenshot showing CubeNTube plugin.

The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....

I don't envy people who start their PhDs now. What they should be trying to do - I think - is to first become confident experts in certain things, and this might involve using as little AI as possible not to become dependent or have their view distorted.

ALC1 Finds a New Foothold on the Nucleosome's Super-Groove
www.biorxiv.org/content/10.1... #cryoEM

Atomic resolution structure of spinach rubisco reveals protons and dynamics www.biorxiv.org/content/10.64898/2025.12.22.696010v1 #cryoEM

Does HDX even work in condensates? This other recent preprint shows pH gradients in organelles, including in membrane-less ones like the nucleolus: doi.org/10.64898/202...
Shouldn't H/D exchange rates on proteins in a condensate depend on the rate of their diffusion through the condensate then?

I also find this very surprising. When it's data points and fit lines, it wouldn't occur to anyone (at least I hope) to only show the lines and never show the points... yet the exact equivalent is easily done with structures, as you describe.

A 3D print of the ALC1-nucleosome structure mentioned in the previous post, with a computer keyboard in the background for scale. The structure is printed in three pieces: the histones (blue), the DNA (grey) and ALC1 (blue). I was told it was pretty difficult to shove the histones into the DNA, since the plastic used to print isn't very flexible. It's looking great anyway. ALC1 is loosely attached, just like in the actual structure; in the 3D print, a piece of double-sided tape allows it to dissociate and bind again.

One thing I had forgotten to post about this whole story: the fine people running our local cryoEM facility in Uppsala made a 3D print of this ALC1-#nucleosome structure and gifted it to me during the facility's end-of-year social event in December. What a sweet attention!

And if you ask for figures, will it give you the equivalent of the infamous lab rat AI figure for the other animals? 🤨

My hero!!! An amazing scientist and a wonderful person!

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 […]

Wonderful! 🤩 Where is it?
And are you into drone photography now??

Cow Tools!

We have lived alongside cows for nearly 10,000 years.
We breed them and exploit them

It is now, only now, that we have discovered THEY CAN USE TOOLS

Here I describe our study

(paper) www.sciencedirect.com/science/arti... in @currentbiology.bsky.social
with @auersperga.bsky.social

Very proud to be part of this project!
This not only is the (nominally) highest resolution non-ApoF cryoEM structure, but also for the first time resolved a ligand and structural hetetogeneity in that resolution range, giving new insights into the Rubisco enzyme mechanism. A nice start for Krios 5!

Figure 6. The super-groove recognition helix of ALC1. (a) View of the minor super-groove at SHL 3.5/-5.5, with the basic residues of the SGRH shown as sticks, and the residue numbers at the start and end of the helix indicated. The color code is the same as in Figure 5. The rest of ALC1 and the nucleosome are translucent for clarity. (b) View of the SGRH looking down the helical axis, with the SGRH colored by conservation. (c) Multiple sequence alignment of ALC1 orthologues verified by structure predictions to have a similar domain architecture as human ALC1, including a putative SGRH.

A closer look at this helix indicates that it is rich in basic residues: Lys and Arg account for 34% of its sequence composition. This already suggests that its function is to interact with DNA. Looking at sequence conservation, it seems like the basic […]

[Original post on fediscience.org]

Figure 5. Structure of an activation intermediate of ALC1 loosely bound to a PARylated nucleosome. (a) Cryo-EM map colored by chain assignment, following the color codes from Figure 1a for the nucleosome and Figure 2a for ALC1. (b) Atomic model, shown in the same orientations and with the same color code as the map shown in panel (a). (c) Structure of the auto-inhibited state. The antibody used for crystallization is shown as a translucent grey surface. From PDB 7EPU. (d) Structure of the intermediate state (dyad view). From this study. (e) Structure of the active state. From PDB 8B0A. In panels (c), (d) and (e), the ATPase residues mutated in the study by (Lehmann et al., 2017) are shown as spheres. In panels (c) and (d), the macro domain residues R857 and R860, found mutated in cancer, are shown as spheres and labeled, and the ADPr-binding pocket of the macro domain is indicated by an ADPr molecule (shown as balls-and-sticks) modeled by structural superimposition of the structure of the Af1521/ADPr complex from PDB 2BFQ (the Af1521 protein is not shown for clarity). In panels (b), (d) and (e), the nucleosome is shown as a translucent surface for clarity.

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 […]

[Original post on fediscience.org]

Figure 3. Flow chart of the image processing workflow. The steps of each distinct stage are highlighted in different colors: pre-processing in purple, particle picking and curation in blue, consensus reconstruction in green, classification of the complexes with tightly bound ALC1 in yellow, classification of the complexes with loosely bound ALC1 in red, and final refinement of the complex with loosely bound ALC1 in pink. For all steps with a circled number, key visuals are presented in Figure 4, and details are provided in section 6.1 Cryo-EM data processing.

Figure 4. Visuals of the key processing steps from Figure 3. The background follows the same color code as in Figure 3. The numbers in parentheses refer to the circled numbers in Figure 3, and details about these are provided in section 6.1 Cryo-EM data processing.

And here is @HRBridges magic explained in a flow chart. ✨

For more info, consult the preprint's methods section and the case study in the CryoSPARC Guide. This is a compact view of the process, showing what worked best. The map we deposited had job number J8039! 😵‍💫

3/5

In 2021, I was involved in a study of the #chromatin remodeler ALC1, a protein involved in the early events of the DNA damage response. This led to a paper summarized in a previous thread: https://fediscience.org/@Guillawme/111534984107819771

We had deposited the raw #cryoEM data to #EMPIAR […]

Figure 1. Structure of the nucleosome. (a) Overview of the nucleosome (disc view). H3 is colored in blue, H4 in green, H2A in yellow, H2B in red, and DNA in grey. From PDB 1AOI. (b) Super-helical locations (SHL) are defined as the points where the major groove faces inward, toward the histone octamer. The base pair at the center of the histone octamer footprint on the DNA is called the dyad and numbered bp 0 / SHL 0 by convention. Each gyre has 7 SHLs, numbered positively on the front gyre and negatively on the back gyre (SHLs with same numbers but opposite signs refer to equivalent locations related by the pseudo 2-fold symmetry of the dyad axis, and a fractional SHL like 1.5 refers to the minor groove between two SHLs, in this example between SHLs 1 and 2). Only the front gyre is displayed here for clarity. From PDB 1AOI. (c) Electrostatic potential of the histone octamer. The H2A-H2B acidic patch is labeled. From PDB 1AOI. (d) The nucleosome’s major and minor super-grooves (gyres view). One of the major super-grooves is indicated by a continuous line (SHL 4/-5). One of the minor super-grooves is indicated by a dashed line (SHL 4.5/-4.5). Super-grooves can be unambiguously referred to by a pair of positive and negative SHLs. The synthetic minor super-groove binder is shown as white spheres. The nucleosome is shown as a surface with the same color code as in panel (a), with the DNA backbone in darker grey. From PDB 1S32.

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 […]

[Original post on fediscience.org]

Atomic resolution structure of spinach rubisco reveals protons and dynamics Photosynthetic organisms sustain life on Earth by storing solar energy in biomass. Central to this process is rubisco, the enzyme that catalyses the fixation of CO2 to ribulose-1,5-bisphosphate, provi...

Atomic resolution structure of spinach rubisco reveals protons and dynamics

@cblikstad.bsky.social

www.biorxiv.org/content/10.6...

RE: https://fediscience.org/@Guillawme/111534984107819771

Something really cool happened to me this year!

@HRBridges re-processed a #cryoEM dataset from some previous work of mine and colleagues (publicly available as EMPIAR-10739; see quoted post below for a summary of this work). She […]

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

ALC1 Finds a New Foothold on the Nucleosome's Super-Groove https://www.biorxiv.org/content/10.1101/2025.11.10.687450v1

On a gruelling hunt for rare associated molecules in your #cryoEM particle stack and not sure where to look?

Discover practical tips and tricks in our new case study using #CryoSPARC v4.7.1 where we find and refine a low-population interaction partner!

guide.cryosparc.com/processing-d...

Thank you for your kind words Marcin!

It's not exactly the same thing: the preprint reports a state found while preparing the case study, but not reported in the case study. 😉