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Jan-Hannes Schaefer

@jhschaef.bsky.social

380 followers 410 following 54 posts

Structural Biology to the rescue. Postdoc with Gabriel Lander at Scripps Research. PhD with Arne Moeller. #cryoEM ❄️🔬 🎹⛳

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Jan-Hannes Schaefer @jhschaef.bsky.social · Aug 1

Check out our new preprint from the @landerlab.bsky.social, Stagg-Lab and Cianfrocco-Lab: CryoSift - An accessible and automated CNN-driven tool for cryo-EM 2D class selection www.biorxiv.org/content/10.1...
Happy testing: cryosift.org #cryoEM #CNN

CryoSift – An accessible and automated CNN-driven
tool for cryo-EM 2D class selection

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Jan-Hannes Schaefer @jhschaef.bsky.social · 3d

I'll try and keep you updated. The story continues.

Jan-Hannes Schaefer @jhschaef.bsky.social · 3d

@maxewilkinson.bsky.social fun little cryo-EM puzzle. I am still pushing the resolution to let ModelAngelo do its magic. My guess was either a common amyloid binder like SAP or an intermediate of Lysozyme-amyloids...

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Jan-Hannes Schaefer @jhschaef.bsky.social · 3d

Thanks @olibclarke.bsky.social I must have overlooked that one and should give it a go.

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Jan-Hannes Schaefer @jhschaef.bsky.social · 3d

Reprocessed ALys Amyloids from EMPIAR-11785 Fändrich Lab

Jan-Hannes Schaefer @jhschaef.bsky.social · 3d

CS workflow for easy testing: github.com/schaefer-jh/...

GitHub - schaefer-jh/CS-amyloids: Amyloid-processing with cryo-SPARC

Amyloid-processing with cryo-SPARC. Contribute to schaefer-jh/CS-amyloids development by creating an account on GitHub.

github.com

Jan-Hannes Schaefer @jhschaef.bsky.social · 3d

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 Jan-Hannes Schaefer

Meytal Landau @meytallandau.bsky.social · 12d

‪We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends
landaulabcssb.bsky.social

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Reposted by Jan-Hannes Schaefer

Oli Clarke @olibclarke.bsky.social · 12d

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.

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Reposted by Jan-Hannes Schaefer

Harry M. Williams @harrywilliams.bsky.social · 20d

❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 21d

Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification https://www.biorxiv.org/content/10.1101/2025.09.14.676144v1

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Reposted by Jan-Hannes Schaefer

Oli Clarke @olibclarke.bsky.social · 21d

Another successful approach to the same problem as HR-HAIR! 🤩 I wonder if a combo might be worth a try - use one frequency band to get perfectly centered particles using 2DTM, then re-estimate orientations using HR-HAIR with a non-overlapping frequency band?

cryoEM papers @cryoempapers.bsky.social · 21d

Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoem

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Jan-Hannes Schaefer @jhschaef.bsky.social · 25d

A great resource. One highlight for me is: "One of the best things about structural biology is visualizing what you are discovering."

Stephanie Wankowicz @stephanieaw.bsky.social · 27d

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

10 Rules for a Structural Bioinformatic Analysis

The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...

chemrxiv.org

Reposted by Jan-Hannes Schaefer

Oli Clarke @olibclarke.bsky.social · 25d

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

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Jan-Hannes Schaefer @jhschaef.bsky.social · 25d

Congrats @olibclarke.bsky.social, great work. I've tried PKA and failed. SPA processing is still an art and lesson in persistence.

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

Magellon has taken off to explore your cryo-EM data! Now out in @iucrj.iucr.org doi.org/10.1107/S205... Congrats to all involved!

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Jan-Hannes Schaefer @jhschaef.bsky.social · Sep 4

I often go back to this striking study: doi.org/10.1126/scie...

Jan-Hannes Schaefer @jhschaef.bsky.social · Sep 4

Uninspired while making figures? Search no more. #science #art

Bird account @dialecticbio.bsky.social · Mar 3

Been thinking about creating a collection of good protein structure figures, as inspiration for my own work.

#1 www.nature.com/articles/s41...

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Jan-Hannes Schaefer @jhschaef.bsky.social · Sep 1

Thanks for sharing @olibclarke.bsky.social. I wonder if many more "hollow" complexes are co-purified with binding-partners. Let's all put more datasets on EMPIAR to revisit processing with new creative approaches like Oli's.

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Jan-Hannes Schaefer @jhschaef.bsky.social · Aug 31

Congrats @olibclarke.bsky.social and team. Such a great idea! Would you share some more CS parameters for the processing-geeks? Maybe via a CS workflow .json?

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Jan-Hannes Schaefer @jhschaef.bsky.social · Aug 29

Our work on "Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned" is now out in Science Advances! Congrats to all involved. www.science.org/doi/10.1126/...

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Reposted by Jan-Hannes Schaefer

Oli Clarke @olibclarke.bsky.social · Aug 22

Was lucky to see this presented at the NYC cryoEM meeting earlier this year - super cool stuff!

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Reposted by Jan-Hannes Schaefer

David B. Sauer @davidbsauer.bsky.social · Aug 15

Di-Gembodies (dimerized nanobodies) for improved and duplexed CryoEM of small and challenging targets!

A collaboration of @cmd.ox.ac.uk, STRUBI, @diamondlightsource.bsky.social, @rosfrankinst.bsky.social

Out now in Nature Chemical Biology @natchembio.nature.com

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

Covalently constrained ‘Di-Gembodies’ enable parallel structure solutions by cryo-EM - Nature Chemical Biology

Disulfide-based dimerization of modified identical and heterologous nanobody scaffolds enables higher-order assembly for high-resolution cryo-electron microscopy structure determination that is widely...

www.nature.com

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Jan-Hannes Schaefer @jhschaef.bsky.social · Aug 14

Thanks Oli, absolutely. Maybe using a resolvability metric like the Q-score? The EMDB auto-validation Q-score could be more visible and added to the RCSB PDB report along with the clashscore.

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Jan-Hannes Schaefer @jhschaef.bsky.social · Aug 14

Good eye. Re-processed AP2 EMPIAR-11604.

Jan-Hannes Schaefer @jhschaef.bsky.social · Aug 14

Thanks for highlighting this great story! @landerlab.bsky.social and I wrote a PREreview about the preprint: prereview.org/reviews/1581...

PREreview of “High-resolution cryo-EM structures of small protein–ligand complexes near the theoretical size limit”

Authored by Jan-Hannes Schäfer and Gabriel C. Lander

prereview.org

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Reposted by Jan-Hannes Schaefer

Eric Topol @erictopol.bsky.social · Aug 6

New @nature.com
The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses
nature.com/articles/s41...

Lithium deficiency and the onset of Alzheimer’s disease - Nature

Lithium has an essential role in the brain and is deficient early in Alzheimer’s disease, which can be recapitulated in mice and treated with a novel lithium salt that restores the physiological level.

nature.com

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