Mariusz Czarnocki-Cieciura

Upper - cryo-EM reconstruction of stomatin AQP1 complex. Lower - reconstruction of stomatin-UT-B complex.

Happy to share a new preprint from the Clarke & Vallese (@fravallese.bsky.social) labs reporting #cryoem structures of two RBC stomatin complexes – with AQP1 & UT-B - continuing the SPFH theme from our recent vault preprint! This was a fun one and has been cooking for a while - read on for more! ⬇️

🧬 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...

That's a wrap! The results of the first #cryoEM heterogeneity challenge are up on biorxiv!
biorxiv.org/content/10.110

Is anyone using a nitrogen gas generator instead of a high-pressure liquid cylinder to feed a cryo-FIB heat exchanger? Just wondering - seems like commercial generators (e.g. for LC-MS) can make ~3-5x the needed flow with a slightly smaller footprint #TeamTomo

Structure from Noise: Confirmation Bias in Particle Picking in Structural Biology

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Structure from Noise: Confirmation Bias in Particle Picking in Structural Biology [new]
Cryo-EM/ET picking bias creates artificial "structure from noise" w/ template matching/NNs. Mitigation strategies exist.

I am very excited to share our recent preprint in which we are structurally investigating macromolecular complexes that contain DNA-binding proteins ICP8 of Herpes Simplex Virus 1 and BALF2 of the Epstein-Barr Virus.
biorxiv.org/content/earl...

Structural insights into DNA annealing and recombination by herpesviral DNA-binding proteins ICP8 and BALF2 https://www.biorxiv.org/content/10.1101/2025.06.25.661518v1

New @ncn.gov.pl OPUS 28 grant for Prof. Marcin Nowotny! 🧬

The project will explore how adenoviruses replicate their DNA - a poorly understood process using cryo-EM and crystallography. Total funding: PLN 3,174,698 🏆

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/

Out now: Another example of how lipidomics led us to see the full(er) picture - enigmatic membrane protein OCIAD1 has a functional role in peroxisomes. Great team work with students and collaborators alike 🧫👩‍🔬🔬

Determining the effects of pseudouridine incorporation on human tRNAs | The EMBO Journal imageimagetRNAs harbour a complex set of modifications which are important for their function. Here, single particle cryo-EM, biophysics, and computational analyses of the effects of pseudouridine inc...

We are very excited about our latest work, which just came out @embojournal.org – www.embopress.org/doi/full/10..... The work @MCB_UJ was driven by Anna Biela and Ting-Yu Lin 林亭妤 in collaboration with @jmbujnicki.bsky.social…a short🧵

Molecular basis of human GABA transporter 3 inhibition Nature Communications - GABA transporters maintain GABA homeostasis and regulate synaptic signaling. Here, the authors determined the cryoEM structures of GABA transporter 3 (GAT3) in its apo form...

I'm excited to share our lab's newest publication on the structure and pharmacology of human GABA transporter 3 @natcomms.nature.com. Much to our surprise, GAT3 adopts an inward-open conformation in complex with the (moderately) selective antagonist SNAP-5114. 💊 🧪 #CryoEM #OpenAccess rdcu.be/ei2KY

Super excited to share this as my first post with the 🦋 world! In my first co-correspondent article, we (@Mayra Borrero @Agnieszka Chacińska @IMOL Institute) look at the roles of lipids in mitochondrial protein import complexes (spoiler: there are plenty!) &call for methods (spoiler: there are few!)

🎉 Incredibly proud to share my first-author paper in
@nature.com! Heartfelt thanks to my mentor @andrzejdziembowski.bsky.social and the brilliant team at DziembowskiLab at @iimcb.bsky.social. More details in the 🧵below ⬇️

IIMCB

🌐Our @nature.com paper is out! Researchers from IIMCB and other Polish institutions show how TENT5A boosts mRNA vaccine efficacy by stabilizing therapeutic mRNAs and enhancing antigen production. A step toward better therapies for cancer and beyond! 🧬

👉Read the story: bit.ly/3XYvQkI

#Nature #mRNA

👋 Hello BlueSky! We’re the International Institute of Molecular and Cell Biology in Warsaw – a research institute at the forefront of life sciences. Our scientists explore the molecular and cellular mechanisms of life, combining curiosity-driven research with scientific and societal relevance.

Structural and biochemical characterization of the 3'-5' tRNA splicing ligases In archaea and metazoa, tRNA exons are ligated by the RNA ligases RtcB and RTCB, respectively. The metazoan RTCB forms a stable complex with four additional subunits, DDX1, FAM98B, CGI99 and ASHWIN. T...

The article was published in JBC and is available here:
www.jbc.org/article/S002...
I wish to thank all the authors from the Nowotny Lab @ IIMCB Warsaw and all the collaborators!

RtcB

Finally, we also performed a chemical cross-linking analysis of the archaeal RtcB protein with its RNA substrate. We observed specific protein-RNA X-links, confirming that the mode of substrate binding is very similar to the AlphaFold3 predictions and observed for the DNA mimic.

Activity assays

We also observed that the tRNA ligase complex with truncated DDX1 helicase showed slightly higher activity. These results suggest that the mobile DDX1 subunit has a negative effect on the ligase activity.

AlphaFold 3 predictions suggest that the tRNA interacts only with a small region of the RtcB protein, which would make it quite mobile. Interestingly, the same region is also predicted to be involved in DDX1 binding.

Structures compared

Despite numerous attempts, we have not been able to obtain a structure with a tRNA substrate. We also did not observe any additional density for the – presumably highly mobile – DDX1 catalytic domains.

Stability and binding tests

To improve the stability and overall behavior of the sample, we reconstituted the complex with truncated variants of the ASHWIN and DDX1 subunits. We verified the functionality of such truncated complex by testing its stability, substrate binding and enzymatic activity in vitro.

I’m happy to share our recent manuscript in which we are structurally and biochemically investigating 3'-5' tRNA splicing ligases, including a #cryoEM structure of the five-subunit D. rerio tRNA ligase complex.
www.jbc.org/article/S002...

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide...

Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...

Structural basis of antiphage defense by an ATPase-associated reverse transcriptase Reverse transcriptases (RTs) have well-established roles in the replication and spread of retroviruses and retrotransposons. However, recent evidence suggests that RTs have been conscripted by cells f...

I am super excited to share our work uncovering the structure and mechanism of an ATPase-associated reverse transcriptase (RT) involved in prokaryotic antiviral defense, now available as a preprint on bioRxiv!🧬🦠🔬
www.biorxiv.org/content/10.1...
🧵👇

🚨New paper🚨Our new study with the lab of Phil Cole uncovers how SIRT6 dynamically adapts structurally and enzymatically to target diverse histone acylations (e.g., H3K27ac) within nucleosomes. @jonmarkert.bsky.social
doi.org/10.1016/j.jb... #Chromatin #SIRT6 #CryoEM

It was a service silicon sample. Next time something more biological I promise!

Thrilled to share the structure of dimerised human PINK1 docked to an endogenous translocase array on the mitochondrial surface, composed of two TOM complexes, bridged by a VDAC2 dimer! Published today in Science www.science.org/doi/10.1126/...

@wehi-research.bsky.social @komanderlab.bsky.social

Fascinating things happening at the IIMCB nowadays! This is one of the first patterns milled with our new TFS Hydra Bio Plasma-FIB, and - most likely - the smallest IIMCB logo ever!