Nilesh Banavali

February Map of the Month: Aca2–RNA

We reprocessed EMPIAR-11918 and achieved 2.76 Å in 50.5 compute hours.

Sub-3 Å at ~40 kDa is a strong example of what modern cryo-EM workflows (and RELION with Blush) can deliver for small targets.

📧 hi@cryocloud.io

#CryoEM #CryoCloud

CryoLike is computationally efficient software for evaluating image-to-structure (or image-to-volume) likelihoods across large image data sets packaged in a user-friendly Python workflow #CryoEM #MolecularModeling #MolecularDynamics doi.org/10.1107/S205...

At long last, the Chlamy chloroplast ribosome hat 🎩 (now renamed the arm 💪) is here to say hello👋! We first spotted this extended structure in green algae a decade ago, and @florentwaltz.bsky.social did beautiful work bringing it into focus! #CryoEM ❄️ #TeamTomo 🔬 #PlantScience 🌾 #ProtistsOnSky 🧪

Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus pubmed.ncbi.nlm.nih.gov/41680142/ #cryoEM

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements pubmed.ncbi.nlm.nih.gov/41711797/ #cryoEM

"QuickStainer": a rapid negative staining device for improved preservation of molecular structure pubmed.ncbi.nlm.nih.gov/41730344/ #cryoEM

A conserved archaeal ribosome-associated factor linking bacterial hibernation and eukaryotic energy sensing https://www.biorxiv.org/content/10.64898/2026.02.22.707292v1

We’re hiring a Microscopy Core Director at the Wadsworth Center!
It's a state position (job stability & PENSION!) in a uniquely academic, research-driven environment 😎
Please share 🙏
statejobs.ny.gov/public/vacan...

Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...

🎉Proud to present our latest paper, out now in Nature Communications: www.nature.com/articles/s41...

RNA Binding Proteins (RBPs) are often full of intrinsically disordered regions (IDRs), but what these regions do during RNA recognition is often unclear. 1/10
#RNA #IDR #RBP

Did you know that because roly polies are terrestrial crustaceans and not actual bugs they breathe through adapted gills even though they live out of water.

Defining the Active Conformation of Typical Protein Kinases Domains from Substrate-Bound PDB Structures Enables Active-State AlphaFold2 Models for All 437 Human Catalytic Protein Kinases

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Defining the Active Conformation of Typical Protein Kinases Domains from Substrate-Bound PDB Structures Enables Active-State AlphaFold2 Models for All 437 Human Catalytic Protein Kinases [new]

A reminder that last baseball season, our newly enshrined women’s singles Olympic gold medalist Alysa Liu threw out the first pitch at a Cardinals game with a pretty sweet double axel on land!

(She looks three feet tall here)

The amyloid packing difference (APD) is a new metric to compare amyloid structures. Analysis of disease-specific structures provides context for the interpretation of APDs for new comparisons. I hope it will be useful! 🤗

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

Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formatio...

www.science.org/doi/10.1126/...

Happy 125th birthday to the Wadsworth Center, and New York State Department of Health! Established on this day in 1901, just 17 years after the publication of Koch's postulates

Science is not truth.
Science is finding the truth.

When science changes its opinion, it didn't lie to you. It learned more.

Boosting origin of life theory, RNA comes close to copying itself Some RNA molecules can create their own mirror images, suggesting similar molecules could have sparked life

Researchers report creating RNAs that can generate a sort of mirror image of themselves and use that template to generate the original.

Learn more: https://scim.ag/46F2BHN

Ribosome biogenesis and homeostasis: in the front line to cope with cellular stress Cells must continuously adapt to both internal and environmental stresses by finely tuning their molecular and metabolic activities. One of the most r…

Fascinated by how cells adapt to a plethora of stimuli?

​This review describes how cells use and modulate #ribosomes to cope with stresses. We discuss the central role of ribosome-associated processes in #cellplasticity, #signaling, #geneexpression and #diseases 🕹

@cbitoulouse.bsky.social

Mechanisms and disease relevance of mitochondrial translation in humans Nature Reviews Molecular Cell Biology, Published online: 13 February 2026; doi:10.1038/s41580-026-00948-2This Review discusses new insights into the intricate regulation of mitochondrial protein synthesis, the pathological consequences of its dysfunction in cancer and immunity, and the complexity of therapeutic targeting of mitochondrial translation.

New Online! Mechanisms and disease relevance of mitochondrial translation in humans

Unveiling hidden variables in stressed bacteria

@cp-cellreports.bsky.social Review by @divyach.bsky.social and @maxencevincent.bsky.social

www.cell.com/cell-reports...

Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species 🦠https://www.biorxiv.org/content/10.1101/2025.05.13.653745v2.full

Ribosome-enriched stress granules form independently of eIF2α phosphorylation and mTOR inhibition when the anticancer drug mitoxantrone is present

doi.org/10.1016/j.jm...

Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay Abstract. New1 is a homologue of the essential yeast translation elongation factor eEF3. Lack of New1 has been shown to induce ribosome queuing upstream of

4 - Still lots to learn about this mysterious factor.
🔗 Read the paper: academic.oup.com/nar/article/...
Funded by @dfg.de via SFB TRR319-RMaP 🙏
#RibosomeBiology #TranslationQC #RNA #Nanopore #Yeast #PhDPosition #DFG #RMaP #New1

RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity - Nature Cas12a3 nucleases constitute a distinct clade of type V CRISPR–Cas bacterial immune systems that preferentially cleave the 3′ tails of tRNAs after recognition of target RNA to induce growth arres...

Our paper is out! Hiding in plain sight among Cas12a nucleases, Cas12a3 cleaves not its RNA target but the 3′ ends of tRNA. Huge thanks to all who made this possible, especially the Beisel lab, Biao & Dirk for the structure, & @sebastianglatt.bsky.social for all things tRNA. doi.org/10.1038/s415...

A corgi's head barely surfacing atop deep snow, against a backdrop of an old wooden fence

I can officially confirm that the snow in NC is roughly one (1) corgi deep

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

Heterologous Substitution of Mycobacterium tuberculosis rRNA in Mycobacterium smegmatis and Its Impact on Antimicrobial Susceptibility pubmed.ncbi.nlm.nih.gov/41594067/ #cryoEM

Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus Lawrence et al. examine how ribosome production in the eukaryotic nucleolus is coordinated by cytoplasmic processes to maintain appropriate ribosome numbers. The authors highlight regulatory inputs from cytoplasmic signaling, mitosis, and cytoplasmic organelles that converge on nucleolar function, and they discuss how disruption of these pathways contributes to human disease.

Online Now: Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus Online now:

Reminder for those applying for #NIH grants using the #ScienCV templates. You can format the text sections using html codes:
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