Jan-Hannes Schaefer

Figure 1. Cryo-EM of abundant protein complexes in native membranes.

Figure 2. Cryo-EM of membrane proteins in vesicles.

Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.

Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.

I've written a review on what I think is an extremely exciting direction in cryo-EM:

Cryo-EM of endogenous membrane proteins in their native lipid bilayer

Open access in Quarterly Reviews of Biophysics:
doi.org/10.1017/S003...

Frontiers | Connecting the dots: deep learning-based automated model building methods in cryo-EM The resolution revolution in single particle cryo-electron microscopy (cryo-EM) has dramatically expanded our structural knowledge of large biomolecular comp...

I can recommend this review doi.org/10.3389/fmol...

ChimeraX screenshot showing CubeNTube plugin.

The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....

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...

Thanks @olibclarke.bsky.social - still too fresh, maybe the bioRxiv link works better? www.biorxiv.org/content/10.6...

ATTR amyloid render from Blender

Microangiopathy in ATTR Cardiac Amyloidosis. Proteomics shows thrombo-inflammation; cleared tissue reveals capillary rarefaction; cryo-EM resolves spearhead fibrils decorated with collagen VI. New preprint from the Kelly, Ye & @landerlab.bsky.social @scripps.edu doi.org/10.64898/202...

Second that. Cryo-EM is still microscopy, so please include micrographs with visible particles.

Thanks, I guess we all needed this.

Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane.

Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane. View from the cytosol.

In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...

Thanks to @actacrystf.iucr.org for highlighting our smart 2D selection tool CryoSift. You can test it yourself here cryosift.org

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier!

I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!

CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!

`Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale The development of methods for low-cost time-resolved cryo-EM using an on-grid mixing strategy is described.

Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale #ElectronMicroscopy #CryoEM #TimeResolvedStudies ... #IUCr https://journals.iucr.org/paper?S2052252525008838

Excited to share a new chapter of my scientific journey in Chris Russo's group — developing a way to freeze proteins faster than they diffuse, paving the way for cryo-EM without air–water interface damage.

🚀 Introducing fully automated data processing for repeat-target #cryoEM.

Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention.

Preprint: www.biorxiv.org/content/10.1...

Thanks @odedrechavi.bsky.social. Even without explicit coverage of structural biology, it did a great job as Reviewer #0 on my latest preprint. Highly recommend www.qedscience.com

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

@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...

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

Reprocessed ALys Amyloids from EMPIAR-11785 Fändrich Lab

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.

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

Amyloid reconstructions from cryoSPARC

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...

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

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 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

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?

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

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

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