In @elife: The Rab7-Epg5 and Rab39-ema modules cooperatively position autophagosomes for efficient lysosomal fusions doi.org/10.7554/eLif...

In @elife: Lipid packing contributes to the confinement of caveolae to the plasma membrane doi.org/10.7554/eLif...

🎉 Congratulations to our postdoc @sergiocruzleon.bsky.social for receiving the 2026 Theory & Computation Postdoctoral Research Award from the Biophysical Society! 🎉 Sergio will present his work at the Theory & Computation subgroup Symposium during the 2026 Biophysical Society meeting.

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Coming Clean and Avoiding Bubble Trouble-Using Detergents Wisely in the Purification of Membrane Proteins for Cryo-EM Studies pubmed.ncbi.nlm.nih.gov/41008622/ #cryoem

#Autophagy and #mTOR papers from last 4 weeks, buildup due to laziness but lots of cool stuff here, have a look! biomed.news/bims-auttor/... biomed.news/bims-auttor/... biomed.news/bims-auttor/... biomed.news/bims-auttor/...

🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture. buff.ly/j3TSIkn

Stability vs flexibility: reshaping archaeal membranes in silico This ‘fundamental’ study characterises the mechanics and stability of bolalipids from archaeal membranes using a minimalist, physics-based computational model. buff.ly/jCnRfkO

Dissipation of lysosome pH impairs formation and collapses existing LPS-induced lysosome tubules in macrophages https://www.biorxiv.org/content/10.1101/2025.09.25.677195v1

PIP4K attenuates PIP5K lipid kinase activity by disrupting membrane-mediated dimerization https://www.biorxiv.org/content/10.1101/2025.09.26.678889v1

#cryoEM 🧪⚛️ Lena’s paper on imaging thick biological sections with STEM is finally published! We started this work almost 10 years ago. After Lena passed in 2023, I spent much of my sabbatical working with Yue and Steve to wrap this up. Also learned a lot about TEM vs STEM dose efficiency

I think this might explain why we tend to see non-vitrified ice more frequently in nucleus than surrounding cytoplasm by cryo-FIB-ET.

Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes | Nature Communications share.google/1S8f1xeAJa0E...

Using cryo-ET, CRN Team Reck-Peterson showed that full-length LRRK2 can oligomerize on microtubules in its autoinhibited state. Both WT-LRRK2 and PD-linked LRRK2 mutants formed filaments on microtubules. 🔗 Read the full #preprint to learn more about their recent research: bit.ly/3VrVNaB

OT-RMSD: A Generalization of the Root-Mean-Square Deviation for Aligning Unequal-Length Protein Structures www.biorxiv.org/content/10.1101/2025.09.23.678064v1 #cryoem

V-ATPase-dependent induction of selective autophagy www.nature.com/articles/s41...

“Side chain densities” … 🫣

FlexConsensus: a tool for merging heterogeneous cryo-EM conformational landscapes into a common latent space to compare similarities and differences. www.nature.com/articles/s41...

Are the lipids associated with static protein structures there as long-lived ligands or an effect of preferential solvation? This computational-experimental framework shows the way! #lipidtime #compchem www.nature.com/articles/s41...

wwPDB has introducing the first 3DEM Model-Map percentile slider (based on Q-score) to validation reports

Alternating Angle Milling Suppresses Streaking Artifacts in FIB-SEM Imaging https://www.biorxiv.org/content/10.1101/2025.09.25.678572v1

Lysosomes signal through the epigenome to regulate longevity across generations | Science www.science.org/doi/10.1126/...

Predicting protein-protein interactions in the human proteome | Science www.science.org/doi/10.1126/...

Structural basis for a filamentous morpheein model of human cystathionine beta-synthase www.biorxiv.org/content/10.1101/2025.09.24.678195v1 #cryoem

If you can't see sidechains, can you really call the resolution 3.3 Å..? 👀 And if you can't see sidechains, how do you know the helical symmetry is right..?

Capturing enzymes in motion pubmed.ncbi.nlm.nih.gov/40988607/ #cryoem

Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on! #TeamTomo #PlantScience 🧪 🧶🧬 🌾 elifesciences.org/articles/105... 1/🧵

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup). A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.

New online: Cryo-EM structures reveal the molecular mechanism of SUMO E1–E2 thioester transfer

gapTrick - Structural characterisation of protein-protein interactions using AlphaFold pubmed.ncbi.nlm.nih.gov/40985612/ #cryoem

Publication bias continues to skew academic literature. In our new @plosbiology.org article, we outline actionable steps for journals, funders & researchers to ensure all results—not only “positive” ones—are valued. A roadmap for more reliable science: journals.plos.org/plosbiology/...

Capturing enzymes in motion The structure and dynamics of the ACE enzyme revealed by #CryoEM and molecular simulations.

Structural remodeling of target-SNARE protein complexes by NSF enables synaptic transmission pubmed.ncbi.nlm.nih.gov/40993127/ #cryoem

Huntingtin binds and bundles F-actin! Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery. We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead! #TeamTomo #CryoET #HTT #actin doi.org/10.1126/scia...

JIP4 and RILPL1 utilize opposing motor force to dynamically regulate lysosomal tubulation url: rupress.org/jcb/article/...

Vacuolar pH regulates clathrin-mediated endocytosis through TORC1 signaling during replicative aging url: rupress.org/jcb/article-...

New research identifies new players involved in LYsosomal Tubulation/sorting driven by LRRK2 (LYTL); RILPL1 is recruited to dysfunctional lysosomes in an LRRK2 kinase activity–dependent manner, facilitated by pRAB rupress.org/jcb/article/...

Dose-efficient cryo-electron microscopy for thick samples using tilt- corrected scanning transmission electron microscopy pubmed.ncbi.nlm.nih.gov/40987871/ #cryoem

Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report From Oct 1, all new 3DEM entries will include the Q-score percentile slider — helping users quickly assess model–map fit quality across EMDB/PDB archives. Read more: www.wwpdb.org/news/news?ye...

Particle Restoration: A Novel Image Processing Framework for Improving Real Cryo-EM Image Quality in Single Particle Analysis pubmed.ncbi.nlm.nih.gov/40986588/ #cryoem

MolViewSpec: describe, share, and reproduce Mol* molecular scenes with a simple extension

Kenneth Gabriel Antenor, Mojca Mattiazzi Usaj et al show that clathrin-mediated #endocytosis becomes less efficient in #aging yeast due to changes in vacuolar pH. Restoring pH or modulating TORC1-Npr1 signaling preserves endocytosis, which may help maintain cell function rupress.org/jcb/article/...

mTORC1 signaling modulate microtubule tyrosination/detyrosination status to regulate lysosome dynamics www.biorxiv.org/content/10.1...

Tilt-corrected bright-field scanning transmission electron microscopy (tcBF-STEM) offers enhanced contrast and dose efficiency for cryo-EM in thick biological specimens. www.nature.com/articles/s41...

Cryo-EM structure of the human MON1A-CCZ1-RAB7A complex provides insights into nucleotide exchange mechanism pubmed.ncbi.nlm.nih.gov/40979223/ #cryoem

Online now - the Forum "The interplay of the cGAS–STING pathway with the lysosome" from Yinfeng Xu and Wei Wan. #InnateImmunity #Lysosome #cGASSTING Read it here: authors.elsevier.com/a/1lpuN_M0e4...

Lysosome-dependent nutrient scavenging underliesstress adaptation during epithelial-to-mesenchymaltransition https://www.biorxiv.org/content/10.1101/2025.09.22.677807v1

ATG16L strikes again! New findings link #lysosome stress and physiology. Alison Klein and Michael Overholtzer @mskcancercenter.bsky.social discuss new study from @thabataduque.bsky.social et al. of the Deretic group (rupress.org/jcb/article/...) in Spotlight: rupress.org/jcb/article/...

Happy to announce "Technical Innovations Using #SerialEM: A Community Meeting", a new format of hybrid meeting David Mastronarde and I are organizing in April 2026. For more info, a preliminary list of speakers, pre-registration etc. visit www.nexperion.net/semcm2026

The SerialEM Python interface has been a huge driver of innovation at the hardware-software boundary in cryo-EM: suddenly the scientist with some programming chops can readily implement their ideas 🥰 This looks like a fantastic meeting!