Internship opportunity! @jackn.bsky.social and I have opened two Summer Intern positions at Genentech to build structural biology agents. If you are a (pre-PhD) #cryoEM or #Xray structural biologist with strong computational skills & motivation, please apply!

Hi fellow membrane protein #StructuralBiology people! Do you use maltoside detergents / model them in your stuctures? Watch out! ⚠️ Most PDB models of LMNG and GDN are wrong ❌, yet continue to be re-used. Spread the word! See more: doi.org/10.1021/acsc... (w. @sebvidalchem.bsky.social ) #cryoEM

A 1.25 A!!! cryo EM structure of rubisco.

We are thrilled to share our new pre-print on the molecular anatomy of nuclear proteasome in human sperm cells! #In-cellcryo-ET + #SPA + #LM! @piotrkolata.bsky.social @a-dsantos.bsky.social, @tomdendooven.bsky.social!! doi.org/10.64898/202...

very unusual - a tRNA regulated anion channel

Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

It’s out! Using cryo-ET in Dicty cells, we take a fresh in situ look at vaults. Surprisingly, we uncover vaults associated with ER and NE membranes, and find that many vaults enclose ribosomes in defined orientations, opening new avenues to their cellular function! www.biorxiv.org/lookup/conte...

The vault associates with membranes in situ https://www.biorxiv.org/content/10.64898/2025.12.12.693869v1

The upcoming relion-5.1 will be able to do old-school 3D subtomos, 3D pseudo-subtomos, as well as 2D stacks. It could be that a true windowing operation in real space removes sufficient low-resolution noise from top/bottom to allow better kickstart of refinement.

Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum | Science www.science.org/doi/10.1126/...

🤯

New online: Atomic models of the Toxoplasma cell invasion machinery

An energy-based model of protein conformational space can be used to predict structure from sequence, sample from the conformational landscape, rank structures, and predict mutation effects. @sokrypton.org www.biorxiv.org/content/10.6...

Mechanistic snapshots of lipid-linked sugar transfer pubmed.ncbi.nlm.nih.gov/41353435/ #cryoem

Train a model to identify circularly-permuted structural homologs, then use it to discover novel pairs of related proteins! @aidenosinetrip1 @abulnaga.bsky.social @sokrypton.org www.biorxiv.org/content/10.1...

Happy to share our cryoEM Ensemble Optimization method! 🎉It infers optimal structures and their weights directly from individual cryoEM images - no maps just physics! with David Sliva-Sánchez, @erikhthiede.bsky.social & Roy Lederman www.biorxiv.org/content/10.6...

Discovery of new AMPA receptor regulators – RNA molecules that act as competitive antagonists causing CNS-related toxicity when intended for treatment of autosomal dominant polycystic kidney disease (ADPKD). Collaboration with Regulus Therapeutic/Novartis! www.nature.com/articles/s41...

Exciting collab with Paul Palme, Peter Imming, & Adrian Richter! Guided by @courbongautier.bsky.social's structure of myco ATP synthase bound to a squaramide, they have made SQAs that are less toxic, more potent, more stable than AstraZeneca's SQ31f #MedChem #TB #NTM pubs.acs.org/doi/full/10....

Cap1 forms a cyclic tetra-adenylate-induced membrane pore during the type III-A CRISPR-Cas immune response pubmed.ncbi.nlm.nih.gov/41292787/ #cryoem

Out today, we can now multiplex receptor mapping at synapses thanks to a dimeric gold nanoparticle label optimized by Hoyoung that's distinguishable from monomers! Dimeric gold nanoparticles enable multiplexed labeling in cryoelectron tomography | PNAS www.pnas.org/doi/10.1073/...

I am pleased to announce the release of ProteinDJ v2! This is a major update that integrates BindCraft into the pipeline as an alternative to RFdiffusion for binder generation. You can try it out here: github.com/PapenfussLab/proteindj #ProteinDJ #BindCraft #ProteinDesign @wehi-research.bsky.social

Frontier structural biology chases low occupancies: weak binders in drug discovery & fleeting intermediates in time-resolved studies. When squeezing SNR, confirmation bias looms – you can see what you hope to see in the noise! Enter METEOR ☄️, our denoising+phasing framework! 1/8

Our latest work : Statins are used to lower plasma cholesterol but often come with muscle-related side effects. Using cryo-EM, we show how multiple statin molecules cooperate to bind RyR1, a calcium release channel mainly found in skeletal muscle. nature.com/articles/s41...

Announcing cryo-EM heterogeneity challenge #2, now dubbed the 2025 Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA)! Join us for a webinar next Friday (Nov 14th) to learn more. Datasets already posted here: heterogeneity.notion.site/challenge #cryoem

Our November issue is available at journals.iucr.org/d/issues/202... On the cover: recent studies demonstrate that the range of samples suitable for cryo-EM single-particle analysis is expanding towards increasingly more native samples. Read the review at shorturl.at/mitjg

We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated. mrc.tal.net/vx/appcentre...

New online: New York City’s structural biology mosaic

OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...

Inhibition mechanism of pancreatic KATP channels by centipede toxins www.biorxiv.org/content/10.1101/2025.10.27.684718v1 #cryoem

A class like no other!! From #AI structure hallucination 🤖 to #CryoEM structure reality 🔬 by @biozentrum.unibas.ch @unibas.ch undergraduate students👩‍🔬👩‍🎓 in just a few weeks! One of their creations is this beautiful flower-shaped tetrameric pore 🌼, a brand new member of the #ProteinCosmos 🧶🧬 🧪

October release of DAQ Score DB of cryo-EM str validation! Now includes 255,199 protein chains from 17,283 EMDB maps. Fig is an example with an entire helix having a residue shift. daqdb.kiharalab.org Easy to use DAQ for structure validation in your paper: em.kiharalab.org

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.

We are excited to share our latest work on GLIC published in @pnas.org, where we developed a #cryoEM data processing strategy that allowed us to isolate and reconstruct multiple asymmetric states, revealing detailed insights into the channel’s activation mechanism. tinyurl.com/mwtb4rpj

Helicon: Helical parameter determination and 3D reconstruction from one image pubmed.ncbi.nlm.nih.gov/41130582/ #cryoem

Finally out in print! Long time project with @olexandr.bsky.social and the PHENIX group. Refinement of X-ray and CryoEM structures, using Machine Learned Potentials as the back end to help fitting. This fulfills the old dream of doing QM refinement, but very very cheap www.nature.com/articles/s41...

Visualizing influenza A virus assembly by in situ cryo-electron tomography www.nature.com/articles/s41...

“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling | Science www.science.org/doi/10.1126/...

Wild

Chris Russo and Anastasiia Gusach have developed a new method to prepare #cryoEM samples that avoids protein damage during freezing Read more: www2.mrc-lmb.cam.ac.uk/a-new-method... #LMBResearch

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon. 🌐 evedesign.bio

**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: [email protected]

Is anyone else having problems with NCBI tools? I'm trying to use the CDD database, and it seems completely broken for requests that worked fine before - not sure if shutdown related?

This looks pretty cool and unexpected.... www.biorxiv.org/content/10.1...

So excited to see this project finally come together after 2+ years of development! I’m proud of my contributions, but this success belongs to the entire Structura team — such a great example of what collaboration and creativity can achieve.

End-to-end automation of repeat-target cryo-EM structure determination in CryoSPARC https://www.biorxiv.org/content/10.1101/2025.10.17.682689v1

Learn how our hunt for the native structure of top antimalarial target PfATP4🧂led to the discovery of PfABP, an unknown essential binding partner, out now! @natcomms.nature.com 👉 rdcu.be/eLRlH 🦠🔬❄️ A team effort led by @mehsehret.bsky.social & Anurag Shukla @akhilvaidya.bsky.social! #cryoEM #malaria

We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale See preprint for: — Ensembles of >12000 full-length human proteins — Analysis of IDRs in >1500 TFs 📜 doi.org/10.1101/2025... 💾 github.com/KULL-Centre/...

Structures of rotary ATP synthase from Thermus thermophilus during proton powered ATP synthesis | Science Advances www.science.org/doi/10.1126/...