Zunlong Ke
@zunlongke.bsky.social
Assistant Professor @UT Austin | Structural Virology | cryo-EM and cryo-ET | Postdoc with John Briggs @MRC_LMB @MPI_biochem | PhD with Elizabeth Wright @GeorgiaTech @Emory
Thrilled to share our latest work, led by @aryantaheri.bsky.social and Julia Peukes! Using cryo-EM and cryo-ET, we reveal how KIF21B’s distal tail engages multiple tubulin dimers along a protofilament, enabling persistent microtubule attachment and crosslinking. www.biorxiv.org/content/10.6...
We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉
Always nice to see some of our work featured in the PDB's Molecule of the Month: pdb101.rcsb.org/motm/319
PDB101: Molecule of the Month: Hantavirus
Family of rodent-borne viruses that can cause severe illness in humans
pdb101.rcsb.org
Reprocessed an old Glacios dataset and pushed this Fab fragment to 3.8 Å resolution! Not a record-breaker by today’s standards, but still pretty satisfying for a C1 particle with only ~48 kDa of ordered mass. #cryoEM
(2/2) "We've identified what we believe is a fundamental mechanism, one that the immune system uses broadly to sustain itself in chronic disease," says MSK cancer immunologist Dr. Andrea Schietinger. Learn more: bit.ly/3RAG4rg
Check out our new poster that highlights the #cryoET workflow, from vitrification and cryo-FIB milling to 3D imaging and computational reconstruction. #TeamTomo 👉 Download the poster: ter.li/erzx0qmh
Structures of asymmetric particles of tick-borne encephalitis virus provide insight into flavivirus assembly and maturation www.science.org/doi/10.1126/...
Structures of asymmetric particles of tick-borne encephalitis virus provide insight into flavivirus assembly and maturation
Flavivirus maturation is enabled by asymmetric rearrangement of the virus envelope proteins.
science.org
From v0.2.0 MissAlignment now has an inference mode where you can apply the trained models from one dataset to a new dataset to skip training time. I haven't tested it extensively, so double check if the results look decent 😉 The program calls changed slightly, see here: github.com/warpem/miss-...
github.com
🔥 Published today, and just in time for summer conferences, here are your guidelines for presenting badly www.nature.com/articles/s41... rdcu.be/fqa92
Excited to share our new preprint! 🧬❄️ by brilliant @mdreimann.bsky.social and great collaborators! Using cryo-ET&EM, we reveal archaeal chromatin in a near-native state: variable-beads-on-a-string fibers shaped by growth phase and histone composition #ArchaeaSky www.biorxiv.org/content/10.6...
Inspired by Utz, I ported the old Briggs lab tools to ChimeraX in a single bundle named Geopickr, with some extra utilities (geopicking on morphometrics surfaces!). I've submitted it to the toolshed, but in the meantime: github.com/baradlab/Geo...
Utz Ermel@uermel.bsky.social · 2mo agoClaude Code is pretty good at writing ChimeraX plugins! This one is almost entirely good context and some prompting: github.com/uermel/chime... Most likely older plugins could be ported over that way relatively easily.
Cryo-ET gives unparalleled views of cellular structures, but targeted sample preparation by cryo-FIB milling has been a constraint. No longer! A new workflow yields close to 100% targeting success for centrioles & other small structures. Read the preprint ⤵️ www.biorxiv.org/content/10.6...
You can take a look at a demo tomogram acquired with the xLPP of apo-ferritin on the cryoET data portal here: cryoetdataportal.czscience.com/datasets/10496 Raw data is of course also available for download!
Dataset
cryoetdataportal.czscience.com
Academic writing should be addressed neither to the public nor to other academics. It should be addressed to a single interlocutor with whom you have a petty rivalry and whose work you are trying to discredit
Direct interactions between the cell’s powerhouses and nuclear pores might channel energy straight into the nucleus, fuelling cell division and differentiation. go.nature.com/43n6Fun
Mitochondria tethered to the nucleus secure its energy supply
Direct interactions between the cell’s powerhouses and nuclear pores might channel energy straight into the nucleus, fuelling cell division and differentiation.
go.nature.com
The results here re 3D classification are quite impressive. Would be interesting to see how much the LPP improves classification of near-native samples with extreme compositional heterogeneity (e.g. derived from cellular fractions)
Laser phase plate improves structure determination of small proteins by cryo-EM
Phase plates can in principle overcome the poor image contrast in electron cryo–microscopy (cryo-EM) and the resulting limits on the structural reconstruction of small proteins. However, previous desi...
science.org
Biohub@biohub.org · 2mo agoIn a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn
Schwartz, Ermel, Owens, Zhao, Peck, Hart, Jensen, Carragher, Kimanius: POPSICLE: Benchmark Datasets for Segmentation and Localization in CryoET https://arxiv.org/abs/2606.10255 https://arxiv.org/pdf/2606.10255 https://arxiv.org/html/2606.10255
Characterization Standard for In-situ Cryo-electron Tomography pubmed.ncbi.nlm.nih.gov/42239035/ #cryoEM
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578
AreTomoLive: a preprocessing pipeline for cryo-ET that streamlines tomographic alignment, reconstruction and contrast enhancement. www.nature.com/articles/s41...
AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput - Nature Methods
AreTomoLive is an accelerated preprocessing pipeline for cryo-electron tomography that streamlines tomographic alignment, reconstruction and contrast enhancement. This pipeline prioritizes automation ...
nature.com
Sub-cellular chemical mapping using correlated cryogenic electron and mass spectrometry imaging online @natmethods.nature.com, led by Hannah Ochner, collaboration with @catfranco.bsky.social and @kiranrpatil.bsky.social labs doi.org/10.1038/s415...
Important new results from lab alumnus Hui Guo @mydange.bsky.social, now a postdoc in the @briggsgroup.bsky.social, out on bioRxiv.
Ed Hutchinson@socialinfluenza.bsky.social · 3mo agoAbsolutely extraordinary work from Hui Gao, John Briggs and co @mpibiochem.bsky.social on the structure of the influenza matrix protein in situ, particularly in filamentous virions. It's beautiful, and answers questions I've been wondering about for twenty years www.biorxiv.org/content/10.6...
Why do influenza viruses make ludicrously long filamentous virions? Probably lots of reasons, but in a new study Lu Liu et al. provide evidence for an appealing hypothesis: filaments are more stable in acidic solutions and hence survive for longer in aerosols www.nature.com/articles/s41...
It's finally out! Molecular architecture of mammalian AP3:ARF1 carriers - a mechanism for lysosomal membrane protein trafficking - from a combination of #biochemistry, #cryoET and #cellbiology 📝 Paper: www.science.org/doi/10.1126/... 🧵 Thread: subsequently #teamtomo #membranetrafficking
Briggs Group@briggsgroup.bsky.social · 3mo agoThe architecture of carriers formed by AP3:ARF1 for lysosomal membrane protein transport: www.science.org/doi/10.1126/.... Work from @jggkaufman.bsky.social, in collaboration with @dgershlick.bsky.social and David Owen. @mpibiochem.bsky.social @thecimr.bsky.social
Recent advances in integrative cryoEM/ET toward visualizing the molecular sociology of cellular organelles pubmed.ncbi.nlm.nih.gov/42134003/ #cryoEM
In situ single-particle Cryo-EM methods: Principle and applications pubmed.ncbi.nlm.nih.gov/42134001/ #cryoEM
Wow - this is just amazing. Hui Guo and colleagues from John Briggs’ lab use cryoEM helical reconstruction to discover how filamentous influenza virion assembly is directed by multiple conformations of M1 - explaining how NA is concentrated at the proximal pole. www.biorxiv.org/content/10.6...
biorxiv.org
