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Reposted by Oli Clarke

Stephan Gruber @gruberlab.bsky.social · 17h

How do SMC complexes load onto DNA to get ready for loop extrusion?

@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️.

Check out the new paper: www.cell.com/molecular-ce...

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Oli Clarke @olibclarke.bsky.social · 18h

no wonder - the Fab-antigen interaction in that structure is only resolved at very low resolution, not at the level of sidechain detail. Probably the starting model is to blame...?

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Reposted by Oli Clarke

Alejandro Llorente, Ph.D. @llorentealejandro.bsky.social · 1d

1/9 🚀 Big news! As a result of 5 years of my PhD, building on a 30-year dream of my PI Dr. Nancy Carrasco, we think we've found a new way to treat cancer! We’ve released our preprint & I'm so excited to share this story! 🧵
www.biorxiv.org/content/10.1...
#Science #proteinengineering #proteindesing

Engineering substrate selectivity in the human sodium/iodide symporter (NIS)

Iodide (I-) uptake mediated by the Na+/I- symporter (NIS) is the first step in the biosynthesis of the thyroid hormones, of which I- is an essential constituent. NIS couples the inward transport of I-...

www.biorxiv.org

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Reposted by Oli Clarke

ttsukaza @ttsukaza.bsky.social · 1d

Our MurJ/LysM paper has been published in Science Advances.

Kohga et al., Sci. Adv. (2025).

This study elucidates, through cryo-electron microscopy, the mechanism by which the small bacteriophage-derived protein LysM inhibits the lipid II flippase MurJ.

t.co/u5ZibBF0kA

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Oli Clarke @olibclarke.bsky.social · 1d

Congrats!!! 🍾 🎉

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Reposted by Oli Clarke

James A. Letts @lettsscience.bsky.social · 1d

Exciting new preprint from the Maldonado Lab @ucdavis.bsky.social
Structure of photosystem I from Giant Kelp!! First brown algae structure of a photosystem and the first structure of any protein from giant kelp a major primary producer, ecosystem defining species.
www.biorxiv.org/content/10.1...

Structure of Photosystem I-FCP from giant kelp uncovers drivers of antenna evolution across the red lineage

Brown algae and other red-algae-derived organisms such as diatoms are major contributors to global CO2 fixation via photosynthesis. To understand the photosynthetic function of brown algae, we obtaine...

www.biorxiv.org

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Reposted by Oli Clarke

Derek Lowe @dereklowe.bsky.social · 1d

Absolutely true. And I’m glad he’s saying it.

AFP News Agency @en.afp.com · 2d

"It is going to be disastrous if this continues"

Nobel Prize physics laureate John Clarke says Trump cuts will 'cripple' US scientific research

u.afp.com/SmAy

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Oli Clarke @olibclarke.bsky.social · 1d

One of my very first placements as an undergrad was with Richard Robson! Growing MOFs with uranyl ions (which sadly failed to crystallize) and organoborate triangles (which worked). Was one of my first experiences with structure determination and I was hooked - so happy to see this!

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Reposted by Oli Clarke

Milot Mirdita @milot.bsky.social · 2d

AFDB v6 is already available in Foldseek!

🚀 search.foldseek.com

foldseek databases Alphafold/UniProt50 afdb50 tmp
foldseek easy-search query.cif afdb50 res.m8 tmp --cluster-search 0/1 (Reps only / all 241M)

Thanks @ebi.embl.org and DeepMind for working with us to make it available to everyone.

EMBL-EBI @ebi.embl.org · 2d

We’re renewing our collaboration with Google DeepMind!

We'll keep developing the AlphaFold Database to support protein science worldwide 🎉

To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.

www.ebi.ac.uk/about/news/t...

🖥️🧬 #AlphaFold
@pdbeurope.bsky.social

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Reposted by Oli Clarke

cryoEM papers @cryoempapers.bsky.social · 2d

ANTIDOTE: A Metadata-Driven Neural Network for Improving CryoEM 3-D Particle Sorting www.biorxiv.org/content/10.1101/2025.10.06.680814v1 #cryoem

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Reposted by Oli Clarke

The Daum Lab @daumlab.bsky.social · 3d

Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail

This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.

www.science.org

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Reposted by Oli Clarke

Sjors Scheres @sjorsscheres.bsky.social · 4d

If you are interesting in developing new algorithms for #cryoEM as a #PhD student or as a #postdoc, then do email or DM me. We have exciting opportunities coming up.

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Oli Clarke @olibclarke.bsky.social · 4d

Turtle yoga in central park 🧘‍♂️

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Oli Clarke @olibclarke.bsky.social · 4d

Also might be worth trying sym expansion, local refinement & Class3D w/out alignments, to test for unexpected pseudosymmetry

Oli Clarke @olibclarke.bsky.social · 4d

Have you tried foldseek using the poly-A from modelangelo as a search model? It does look similar to a phage tail at first glance, e.g. the C6 one here: www.cell.com/structure/fu...

Cryo-EM structure of flagellotropic bacteriophage Chi

Sonani et al. report the structure of bacteriophage χ using cryo-EM, revealing its capsid, neck, tail, and tail-tip organization. Unique proteins in the neck and tail tip, including a trimeric assembl...

www.cell.com

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Reposted by Oli Clarke

Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 4d

Another day, another paper by the Baker's lab

bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 7d

De novo design of RNA and nucleoprotein complexes https://www.biorxiv.org/content/10.1101/2025.10.01.679929v1

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Oli Clarke @olibclarke.bsky.social · 4d

Also - for the more flexible filaments, thinking mostly about the weird lysozyme tube - did you try helical sym expansion followed by local refinement with a mask around the central section? I’ve found this to help quite a lot with flexible filaments

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Oli Clarke @olibclarke.bsky.social · 4d

… and I also think there is a pretty balanced discussion in this preprint of the limitations of CS with respect to RELION for processing amyloid samples (and validation issues etc)

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Oli Clarke @olibclarke.bsky.social · 4d

Fantastic work Jan! Have you had a go at the FIA filament from the BLUSH paper? I haven’t been able to get that one to go in CS, but I am far from an amyloid expert

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Oli Clarke @olibclarke.bsky.social · 4d

I think this is a bit of a false dichotomy Sjors - not everyone needs to (or is able to) develop new algorithms, and there is a place for learning how to use existing software optimally for specific types of samples, whether closed source or not - I don’t see why this has to be an either/or…

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Reposted by Oli Clarke

Jan-Hannes Schaefer @jhschaef.bsky.social · 5d

Helical Reconstruction of Amyloids in cryoSPARC?
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...

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Reposted by Oli Clarke

cryoEM papers @cryoempapers.bsky.social · 5d

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail pubmed.ncbi.nlm.nih.gov/41042861/ #cryoem

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Reposted by Oli Clarke

Edward T Eng @edwardteng.bsky.social · 5d

Muyuan Chen has turned structural biology into an immersive experience with his new video game Meowtabolism, now available on Steam.
Try the demo here: store.steampowered.com/app/4045010/...
Give Muyuan feedback: steamcommunity.com/app/4045010
#ScienceGaming #StructuralBiology #CryoEM #STEMOutreach

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Reposted by Oli Clarke

bioRxivpreprint @biorxivpreprint.bsky.social · 9d

GABAA receptor gating imaged on the millisecond timescale https://www.biorxiv.org/content/10.1101/2025.09.29.679341v1

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Oli Clarke @olibclarke.bsky.social · 5d

Bit of a mix - have bought 4 workstations over the years connected by a NAS. Our latest is 4xA6000, threadripper, 512G RAM, as much fast SSD as I could fit - have been happy with that one

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