Jason Yu
banner
jasonyjc.bsky.social
Jason Yu
@jasonyjc.bsky.social
PhD Candidate in the Rubinstein Lab
@utoronto.ca @sickkidsto.bsky.social 🇨🇦
I study mycobacteria and do cryo-EM.
Reposted by Jason Yu
Long in the making, but happy to present the Chlamydomonas chlororibosome!
Cryo-ET🔬reveals a large new domain on the small subunit, built from multiple extensions in conserved ribosomal proteins.
bioRxiv 📖: shorturl.at/q44tG
This suggests greater chlororibosome diversity than expected!
1/n 🧵
February 10, 2026 at 8:35 AM
Reposted by Jason Yu
@structurabio.bsky.social and @sickkidsto.bsky.social CryoSPARC workshop in Toronto!
April 30/May 1st 2026.
Part of the Canadian Cryo-EM Nexus.
Please register here: sickkids.cventevents.com/event/a0aebb...
January 30, 2026 at 3:41 PM
Reposted by Jason Yu
🚀 CryoSPARC v5.0 BETA is here!

We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread!

Full changelog: cryosparc.com/updates/v5.0.0
January 27, 2026 at 8:36 PM
Reposted by Jason Yu
Congratulations to the new Doctor of Philosophy @courbongautier.bsky.social on a spectacular PhD defense following a groundbreaking PhD!
Thanks to external examiner Damian Ekiert from JHU and the rest of the examining committee.
Next stop, Oxford University for a postdoctoral fellowship.
🇫🇷🇨🇦🇬🇧
January 9, 2026 at 2:56 AM
Reposted by Jason Yu
In Jan 2006 I started my dream job: running my own research group at The Hospital for Sick Children in my home town, Toronto. Stephanie Bueler started as lab manager on Day 1.
Many students, postdocs, papers, and microscopes later we're still going strong - and Stephanie is still putting up with me!
January 6, 2026 at 12:28 AM
Reposted by Jason Yu
We’re excited to share our latest study that reshapes our understanding of Mycobacterium tuberculosis (Mtb) lipid composition, with major implications for drug discovery, immunity, and vaccine development.

www.nature.com/articles/s41...

A thread.
Mycobacterium tuberculosis overcomes phosphate starvation by extensively remodelling its lipidome with phosphorus-free lipids - Nature Communications
Here, the authors show that Mycobacterium tuberculosis manipulates lipid metabolism to overcome host restriction, by remodelling its lipidome and utilising host lipids as an alternative phosphate sour...
www.nature.com
December 22, 2025 at 1:11 PM
Reposted by Jason Yu
Mycobacterium tuberculosis is an outlier in many ways. One of them is keeping a high degree of functional redundancy despite its obligate pathogen lifestyle. In this review, we reflect on the biological meaning of M. tuberculosis functional redundancies.

journals.plos.org/plospathogen...
Essential redundancies fuel Mycobacterium tuberculosis adaptation to the host
Redundancy in biology is, at a glance, counterintuitive because if the function of two gene products completely overlaps then, throughout the course of evolution, one of the genes will likely accumula...
journals.plos.org
December 7, 2025 at 12:07 PM
Reposted by Jason Yu
Does this create an Achilles’ heel, and can you drug it? Turns out: yes.

Congrats to Barbara, Vanisha, Liz, and the rest of the team.

www.nature.com/articles/s41...
Transcription co-inhibition alters drug resistance evolution and enhances Mycobacterium tuberculosis clearance from granulomas - Nature Microbiology
Targeting two distinct steps of the transcription process yields synergistic antibiotics that kill non-replicating Mycobacterium tuberculosis and reduce drug resistance.
www.nature.com
December 3, 2025 at 11:10 AM
Reposted by Jason Yu
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....
Design, Synthesis, and Biological Evaluation of Mono- and Diamino-Substituted Squaramide Derivatives as Potent Inhibitors of Mycobacterial Adenosine Triphosphate (ATP) Synthase
Amides of squaric acid are new drug candidates with activity against mycobacteria. Like the approved drug bedaquiline, these compounds achieve efficacy by inhibiting mycobacterial ATP synthase. Howeve...
pubs.acs.org
November 27, 2025 at 11:53 PM
Reposted by Jason Yu
🚀 Hiring: Cryo-EM Application Scientist, Marketing!

Develop and deliver high-impact scientific marketing content, illustrate the value of new #CryoSPARC features and #cryoEM advances, and help scientists understand how our tools can help solve their problems.

structura.bio/careers/appl...
Structura Bio | Structura Bio
structura.bio
November 20, 2025 at 9:00 PM
Reposted by Jason Yu
#NewResearch

A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated C. difficile infection in mice.

#MicroSky 🦠💊

www.nature.com/articles/s41...
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - Nature Microbiology
A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated Clostridioides difficile infection in mice.
www.nature.com
November 18, 2025 at 2:07 PM
Reposted by Jason Yu
With the Wilmanns lab @embl.org we reveal cryoEM structures of an essential, bifunctional acyl-CoA carboxylase from mycobacteria. @wertheimufscripps.bsky.social

This ~ 600 kDa enzyme is asymmetric, rotatory, has unusual stoichiometry, and unique E5 subunits.

www.biorxiv.org/content/10.1...
www.biorxiv.org
November 17, 2025 at 1:38 PM
Reposted by Jason Yu
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
November 5, 2025 at 1:29 PM
Reposted by Jason Yu
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...
October 30, 2025 at 1:33 PM
Reposted by Jason Yu
New lab preprint!
@zestytoast.bsky.social tagged a scarce mycobacterial protein in M. smegmatis with TwinStep but got… something? @kjamali.bsky.social's ModelAngelo built models & @martinsteinegger.bsky.social's FoldSeek IDed them as the biotin-containing MCC & LCC complexes
🧵
tinyurl.com/ukny4ptz
October 30, 2025 at 3:21 AM
Reposted by Jason Yu
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!
October 26, 2025 at 10:40 PM
Reposted by Jason Yu
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
Endogenous structure of antimalarial target PfATP4 reveals an apicomplexan-specific P-type ATPase modulator
Nature Communications - Here, the authors present the 3.7 Å cryoEM structure of native sodium efflux pump PfATP4 from Plasmodium falciparum, revealing a bound protein that they term...
rdcu.be
October 20, 2025 at 12:55 PM
Reposted by Jason Yu
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️

www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 6:26 AM
Reposted by Jason Yu
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...
October 5, 2025 at 4:16 AM
Reposted by Jason Yu
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
September 29, 2025 at 3:01 PM
Reposted by Jason Yu
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
September 28, 2025 at 9:16 PM
Reposted by Jason Yu
Finally in @nature.com 🎉
We uncovered step-wise mTORC1 activation on membrane: RAG–Ragulator recruits, RHEB pushes closer, and direct membrane contacts by RAPTOR + mTOR trigger full kinase activity.👉 The membrane is not just a platform — it’s part of the mechanism.
www.nature.com/articles/s41...
Structural basis for mTORC1 activation on the lysosomal membrane - Nature
Cryo-electron microscopy was used to study human mechanistic target of rapamycin complex 1 (mTORC1) activation on lysosomal membranes, showing progressive recruitment by RAG–Ragulator, RHEB and R...
www.nature.com
September 17, 2025 at 9:35 PM
Reposted by Jason Yu
We finally wrote up the paper for LocScale-2.0.

edu.nl/pvhxv

Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.

Code: cryotud.github.io/locscale/

Work by @alok-bharadwaj.bsky.social and Reinier.
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.

Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.

cryotud.github.io/locscale/
September 15, 2025 at 7:39 AM
Reposted by Jason Yu
This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x
September 13, 2025 at 12:05 AM
Reposted by Jason Yu
🧬 Transcription elongation by RNA polymerase II relies on a web of elongation factors. Our new work shows how IWS1 acts as a modular scaffold to stabilize & stimulate elongation. Fantastic work by Della Syau! www.biorxiv.org/content/10.1...
August 29, 2025 at 10:14 AM