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Dan Grabarczyk

@dangrabarczyk.bsky.social
542 followers 873 following 7 posts

Structural biologist - currently ubiquitin ligases, previously DNA replication and bacterial metabolism Research Associate - Clausen Lab, IMP Vienna

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Reposted by Dan Grabarczyk
Molecular Cell @cp-molcell.bsky.social · 22/09/2026
Molecular mechanism of HUWE1-HAPSTR1-USP7-mediated ubiquitin chain amplification on nuclear proteins
dlvr.it
Molecular mechanism of HUWE1-HAPSTR1-USP7-mediated ubiquitin chain amplification on nuclear proteins
Yatskevich et al. show that HUWE1 amplifies existing ubiquitin tags through chain elongation and branching. A cryo-EM structure reveals multivalent HUWE1-USP7 assembly and reciprocal regulation, while HAPSTR1 tunes substrate capture by engaging HUWE1 ubiquitin-binding motifs, defining a coordinated system for short-lived nuclear protein turnover.
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Reposted by Dan Grabarczyk
Thomas Arnesen @natmachinery.bsky.social · 21/09/2026
Coenzyme A biosynthesis is regulated by two distinct Ubiquitin E3 ligase complexes | UBR4-KCMF1 and MKLN1-CTLH independently converge on a common N-terminal MK Arg/N-degron to promote PANK degradation and restrict CoA biosynthesis | @ispt-proteinterm.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Parallel Arg/N-degron recognition systems regulate coenzyme A biosynthesis
Coenzyme A (CoA) is an essential metabolic cofactor whose biosynthesis is controlled by pantothenate kinases (PANKs), the rate-limiting enzymes in CoA synthesis. Although CoA production is extensively...
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Reposted by Dan Grabarczyk
IMP @impvienna.bsky.social · 03/09/2026
IMP postdoc Elias Adriaenssens has received an ERC Starting Grant worth close to €1.5 million. He will study how cells decide when to dispose of their organelles—and how they prevent healthy ones from being destroyed: bit.ly/4zUBQMy
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Reposted by Dan Grabarczyk
Frederica Theodoulou @freddietheodoulou.bsky.social · 01/09/2026
Ever wondered why mutating BIG/AtUBR4 causes pleiotropic 🌿 phenotypes? Find a whistle stop tour of the literature in our latest review, with expert structural insight from @dangrabarczyk.bsky.social and @clausenlab.bsky.social academic.oup.com/jxb/advance-...
academic.oup.com
Decoding BIG: how one protein influences multiple pathways
Abstract. A major strength of forward genetic screens is their unbiased nature: the plant reveals which genes underlie a physiological process. Yet this st
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Reposted by Dan Grabarczyk
Rhys Grinter @rhyswg.bsky.social · 18/08/2026
Out now in @natmicrobiol.nature.com: Bacillus subtilis builds protein filaments that act as a pseudomembrane, pulling quinone out of the bilayer and carrying it into the cytosol for reduction by NADH dehydrogenase, well away from the membrane itself. doi.org/10.1038/s415... 1/5
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Reposted by Dan Grabarczyk
Elliott Lab @elliottlab.bsky.social · 14/08/2026
Huge effort from the Lab into the mechanics of the mysterious #ubiquitin like protein FAT10 – taking structural snapshots of FAT10 activation by UBA6 and transfer onto UBE2Z plus really interesting insights into InsP6 regulating FAT10 conjugation pathways: www.nature.com/articles/s41...
nature.com
Structural determinants for FAT10 activation and transfer from UBA6 to E2 enzymes - Nature Communications
Cryo-EM captures FAT10 activation and transfer from UBA6 to E2 UBE2Z, revealing FAT10 monopolises UBA6. Efficient transfer requires E2 engagement of both FAT10 UBL domains, particularly UBL2, and co-o...
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Reposted by Dan Grabarczyk
Sophia Paul @sophia-pa.bsky.social · 08/07/2026
Excited to share my paper! 🥳 Today in #Nature we reveal an 8 MDa Hdr electron bifurcating super-assembly in class I methanogens that couples the first and last steps of hydrogenotrophic methanogenesis. A lineage-specific adaptation to anaerobic niches. www.nature.com/articles/s41...
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Reposted by Dan Grabarczyk
trisre.bsky.social @trisre.bsky.social · 06/07/2026
1/ Happy to share our preprint! The Mtr complex catalyses the second-to-last step of the methanogenesis and is an essential bioenergetic machine in most methanogenic archaea. Anaerobic cryo-EM of Mtr reveals a nitrogenase-like metallocluster bound at its active site! www.biorxiv.org/content/10.6...
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Ben Engel @cellarchlab.com · 03/07/2026
Super excited to launch this search for a new endowed professor at the @biozentrum.unibas.ch! Join us to build a research cluster in Climate Biophysics! 🌍🌊🌾🔬🧪 This is a unique opportunity to create a community in Basel🇨🇭working together on this timely topic! ⏳🌡️ Questions? Please reach out! 👩‍🔬👨‍🔬
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erzbergerlab.bsky.social @erzbergerlab.bsky.social · 02/07/2026
Membrane protein solubilization and structure determination using de novo–designed proteins | Science www.science.org/doi/10.1126/...
science.org
Membrane protein solubilization and structure determination using de novo–designed proteins
Developing therapies and vaccines against integral membrane proteins is hindered by their extensive hydrophobic surfaces, which complicate production and structural analysis. Here, we describe a gener...
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Reposted by Dan Grabarczyk
Silvia Ramundo @sramundo.bsky.social · 24/06/2026
1/7 New preprint: we found that Chlamydomonas carries a giant and unexpectedly elaborate chloroplast RNA polymerase with 12 previously unknown subunits, overturning the idea that the complexity of this organellar enzyme emerged during plant terrestrialization! www.biorxiv.org/content/10.6...
biorxiv.org
The structure of a 2-MDa chloroplast RNA polymerase reveals unexpected evolutionary complexity
Transcription in chloroplasts depends on the Plastid-Encoded RNA polymerase (PEP), a bacterial-derived enzyme whose catalytic core remains encoded by the highly reduced genome inherited from the cyano...
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Reposted by Dan Grabarczyk
Thomas Arnesen @natmachinery.bsky.social · 23/06/2026
Structural and mechanistic insights into the UBR4-KCMF1-Calmodulin complex @ispt-proteinterm.bsky.social academic.oup.com/proteincell/...
academic.oup.com
Structural and mechanistic insights into the UBR4-KCMF1-Calmodulin complex
Dear Editor,
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Reposted by Dan Grabarczyk
Structura Biotechnology @structurabio.bsky.social · 09/06/2026
🔍 Sample heterogeneity is both a challenge and an opportunity in #cryoEM data processing. In our latest #CryoSPARC case study we explore EMPIAR-10927, a dataset with acetogenin-bound mitochondrial Complex I, that reveals many more complexes according to the data processing strategy 👉 bit.ly/4uihh8V
bit.ly
Case Study: Discrete heterogeneity in a sample of Acetogenin-bound complex I (EMPIAR 10927) | CryoSPARC Guide
Processing EMPIAR-10927 including separating targets using Per-particle scales or custom settings in Ab-Initio Reconstruction, and using 3DVA to guide sub-classification choices.
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Reposted by Dan Grabarczyk
Rémi Fronzes @fronzeslab.bsky.social · 26/05/2026
New preprint. In S. sanguinis, a C5a peptidase-like protease (ScpH) polymerizes along eDNA, turning it into a catalytic biofilm scaffold. Great work from @robinanger.bsky.social in our lab, with Pelicic lab @lcbofficiel.bsky.social www.biorxiv.org/content/10.6...
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Reposted by Dan Grabarczyk
Clausen Lab @clausenlab.bsky.social · 21/05/2026
Open Postdoc Position - Giant E3 ligases: mysterious mechanisms & non‑protein substrates. Interested? Join us to uncover how these molecular giants tag lipids, RNAs, sugars beyond proteins, on organelles and pathogens, to defend the cell. Details & Application here www.imp.ac.at/career/open-...
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qiangguo.bsky.social @qiangguo.bsky.social · 22/04/2026
Preprint with new server~ Using in situ cryo-ET, we identify a previously uncharacterized higher-order architecture of urate oxidase in mouse liver. langtaosha.org.cn/lts/en/prepr...
langtaosha.org.cn
A conserved helix-tiling architecture of urate oxidase organizes metabolism in peroxisomes
Cells organize metabolism within a crowded intracellular milieu, yet the structural logic and functional consequences of supramolecular enzyme assemblies in vivo remain poorly defined. Here, using in
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Reposted by Dan Grabarczyk
Carter Lab @carter-lab.bsky.social · 24/03/2026
Excited to share our work on the structure and function of cytoplasmic lattices within mouse embryos. A collaborative effort with @niakanlab.bsky.social and work led by @kashishsingh.bsky.social and @inaharasimov.bsky.social . It is now out on BioRxiv: www.biorxiv.org/content/10.6...
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Jacob Corn @jcornlab.bsky.social · 18/03/2026
Proper organelle regulation during mitosis is a must, but how do membrane-less condensates like PML bodies behave during cell division? In work led by Eric Aird, we found the balance of speckled proteins SP110 & SP100 to be the key. doi.org/10.1038/s415...
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Reposted by Dan Grabarczyk
Ian Kelsall @iankelsall.bsky.social · 05/03/2026
Registration now open for #EMBOUbiquitin. meetings.embo.org/event/26-ubi... Childcare, accessibility, and travel grants available. #ubiquitin #TargetedProteinDegradation #Proteostasis #UBL
meetings.embo.org
Ubiquitin and ubiquitin-like proteins in health and disease
The ubiquitin system is fundamental to virtually all biological processes and is essential for maintaining cellular and organismal homeostasis. Recent technological advances are revealing new roles f…
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Reposted by Dan Grabarczyk
Lori Passmore @lapassmore.bsky.social · 25/02/2026
We are excited to be recruiting a new tenure track group leader in the Structural Studies Division at MRC LMB! It is an amazing place to start your own lab. @mrclmb.bsky.social Please get in touch if you have any questions. www.nature.com/naturecareer...
nature.com
Research Group Leader Tenure Track - Structural Studies - LMB 2775 - Cambridge, Cambridgeshire (GB) job with MRC Laboratory of Molecular Biology (LMB) | 12854636
Research Group Leader Tenure Track Starting Salary £67,979 to £76,868 per annum MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laborato...
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Reposted by Dan Grabarczyk
ChimeraX @chimerax.ucsf.edu · 24/02/2026
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....
ChimeraX screenshot showing CubeNTube plugin.
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Reposted by Dan Grabarczyk
versteegga.bsky.social @versteegga.bsky.social · 17/02/2026
Our paper is out in @natcomms.nature.com! APOBEC3s drive mutagenesis in cancer. We uncover a novel pathway keeping them in check. The key is APOBEC3 binding of cellular RNAs, which simultaneously controls their nuclear localization and shields them from degradation. Read it here: rdcu.be/e4qaa
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Reposted by Dan Grabarczyk
IMP @impvienna.bsky.social · 11/02/2026
To regulate gene activity, proteasomes - waste disposal machines of cells - must enter the nucleus. IMP Researchers now show how the adaptor protein AKIRIN2 helps ferry this massive complex through the nuclear pore: www.nature.com/articles/s41467-026-…
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Dan Grabarczyk @dangrabarczyk.bsky.social · 11/02/2026
Some cool E3 ligase structures here with calmodulin-mediated oligomerisation. Also interesting collection/processing to deal with preferred orientation. www.biorxiv.org/content/10.6...
biorxiv.org
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Institute of Molecular Biology (IMB) @imbmainz.bsky.social · 06/02/2026
@lorenzoorts.bsky.social previously worked as a postdoctoral fellow at @impvienna.bsky.social in Austria. She will establish a new lab at IMB to investigate how mRNA translation is activated in the early embryo. Welcome to IMB Laura! 💐 Read more here: www.imb.de/about-imb/ne...
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Sylvie Callegari @sylviecallegari.bsky.social · 04/02/2026
After a long (but fun!) postdoc journey, I am very excited to share that I will start my own lab in the Ubiquitin Signalling Division at WEHI. We will study how ubiquitin controls mitochondrial health and its role in neurodegenerative disease. Hiring soon!
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Jakob Farnung @jakobfarnung.bsky.social · 06/01/2026
When RNA Degradation 🤝 meets 🤝 Protein Degradation! tinyurl.com/E3TDMD In a collaboration of @bartellab.bsky.social and Schulman lab, we show that, in target-directed microRNA degradation (TDMD), 2-RNA-factors recruit an E3 ligase and induce the degradation of not only a protein but also RNA (1/5).
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Reposted by Dan Grabarczyk
Stephen Royle @steveroyle.bsky.social · 16/12/2025
Vaults. They are cell biology's greatest puzzle! This preprint from Martin Beck's lab shows them docked on ER membranes with a ribosome inside. What on earth is going on there?? #CellBiology #WTFology www.biorxiv.org/content/10.6...
biorxiv.org
The vault associates with membranes in situ
The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using ...
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Oli Clarke @olibclarke.bsky.social · 11/12/2025
🤯
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Rachel O'Dea @rnidhea.bsky.social · 08/12/2025
SAVE THE DATE! The EMBO workshop "Ubiquitin and Ubiquitin-like proteins in Health and Disease" will be on September 2026. Exciting line up of talks and an amazing location! Organised by @kulathu.bsky.social, @merbllab.bsky.social, @simonapolo.bsky.social, Claudio Joazeiro. Registration open soon.
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Reposted by Dan Grabarczyk
Marcin J. Suskiewicz @msuskiewicz.eurosky.social · 17/11/2025
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
rdcu.be
Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
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Reposted by Dan Grabarczyk
Nature Chemical Biology @natchembio.nature.com · 14/11/2025
A new Review discusses how degrons of different types, with an emphasis on high-order structural ones, regulate substrate-E3 interactions and how their dysregulation is linked to human diseases www.nature.com/articles/s41...
nature.com
Degrons and degradation signals beyond short linear motifs - Nature Chemical Biology
Degrons are degradation signals in target proteins to direct recognition and degradation by the ubiquitin–proteasome system. Wang et al. introduce degrons of different types, with an emphasis on high-...
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Reposted by Dan Grabarczyk
Tanmay Bharat @tbharat-lab.bsky.social · 07/11/2025
An Asgard archaeon with internal membrane compartments Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors! www.biorxiv.org/content/10.1...
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Max Perutz Labs Vienna @maxperutzlabs.ac.at · 31/10/2025
📢 Open Call! The Max Perutz Labs invite applications for a Full Professorship in Integrative Structure Biology with a focus on in situ structural biology using cryo-electron tomography (cryo-ET) and related methods. More details ➡️ tinyurl.com/brswbymu
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Waggoner Lab @labwaggoner.bsky.social · 17/10/2025
Split-site ubiquitination gives ZNFX1 new power in RNA defense @cellcellpress.bsky.social www.cell.com/molecular-ce... www.sciencedirect.com/science/arti...
cell.com
Split-site ubiquitination gives ZNFX1 new power in RNA defense
Recent work by Grabarczyk et al. uncovers the molecular mechanism by which ZNFX1, an interferon-stimulated gene, employs a novel split-site E3 ligase domain structure to ubiquitinate both protein lysi...
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Arne Elofsson @handle.invalid · 02/10/2025
Elaborate machinery for inserting proteins into the outer membrane of bacteria www.nature.com/articles/d41...
nature.com
Elaborate machinery for inserting proteins into the outer membrane of bacteria
Bacteria in the gut use an unusual molecular apparatus to insert complex proteins into their outer membrane.
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Reposted by Dan Grabarczyk
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 19/09/2025
Structure and substrate recognition by the Twin-arginine translocation (Tat) pathway core complex www.biorxiv.org/content/10.1101/202…
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Dan Grabarczyk @dangrabarczyk.bsky.social · 27/09/2025
Thanks a lot to Yiyun Song @natchembio.nature.com for highlighting our ZNFX1 paper. www.nature.com/articles/s41...
nature.com
Dimerization for activation - Nature Chemical Biology
Nature Chemical Biology - Dimerization for activation
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Lori Passmore @lapassmore.bsky.social · 27/09/2025
We have an open post-doc position in my group to study mRNA cleavage and polyadenylation using biochemical reconstitution and cryoEM. Please get in touch if you are interested in joining this amazing team! 🔬🧬🤩 #RNA #cryoEM
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Caitie McCafferty @computingcaitie.bsky.social · 23/09/2025
I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪
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Laura Lorenzo Orts @lorenzoorts.bsky.social · 15/09/2025
I am excited to announce that I will be moving to IMB Mainz next year! The Winter call for the IPP PhD program is now open; if you are interested in maternal #mRNA regulation and #translation in early vertebrate development, please apply! Deadline: 16 October. More info: www.imb.de/students-pos...
imb.de
Laura Lorenzo Orts
IMB Mainz
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Reposted by Dan Grabarczyk
Fletcher Lab @fletcherlab.bsky.social · 08/09/2025
Pre-print: our description of RZ affiliate ZNFX1 is now online. On binding viral RNA, ZNFX1 generates parallel Ub currents, coordinating Ub-dependent RNA silencing and aggregate resolution. Huge effort from first authors Dan Squair and @eilidhrivers.bsky.social www.biorxiv.org/content/10.1...
biorxiv.org
ZNFX1 uses two-component ubiquitin circuitry to quarantine viral RNA
The detection of viral RNA inside cells triggers a diverse range of antiviral responses, including global translation inhibition, interferon secretion and RNA sequestration. Mutations in the gene ZNFX...
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Reposted by Dan Grabarczyk
IMP @impvienna.bsky.social · 28/08/2025
Researchers around @clausenlab.bsky.social & @dangrabarczyk.bsky.social have unveiled the three-dimensional structure of UBR4, a giant protein complex that safeguards cells by targeting defective proteins for destruction—offering fresh insights into health & disease. www.science.org/doi/10.1126/...
imp.ac.at
Inside the cell’s recycling hub: unveiling the architecture of UBR4
Researchers from the lab of Tim Clausen and collaborators have unveiled the three-dimensional structure of UBR4, a giant protein complex that safeguards cells by targeting defective proteins for destr...
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Dan Grabarczyk @dangrabarczyk.bsky.social · 28/08/2025
Glad to share the final version of our story about the UBR4 complex, an E4 ligase protein quality control hub @science.org. Now with more cryo-EM structures and a deeper dive into substrate recognition, especially escaped mitochondrial proteins @clausenlab.bsky.social www.science.org/doi/10.1126/...
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IMP @impvienna.bsky.social · 28/08/2025
Scientists uncovered how the immune protein ZNFX1 enables cells to walk the fine line between fighting infection & avoiding autoimmune damage. ZNFX1 can ubiquitinate & compact host & viral RNA into molecular condensates, extending ubiquitin biology to RNA itself. More: www.imp.ac.at/news/article...
imp.ac.at
ZNFX1 compacts and tags RNA to keep immunity in check
Tim Clausen’s lab at the IMP and collaborators have uncovered how the ancient immune protein ZNFX1 enables cells to walk the fine line between fighting infection and avoiding autoimmune damage. The te...
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Dan Grabarczyk @dangrabarczyk.bsky.social · 27/08/2025
Happy to share our work on the structure and function of the unusual E3 ligase ZNFX1 @cp-cell.bsky.social. It uses a nucleic acid-activated transthiolation mechanism, ubiquitinating and clustering RNA to protect cells in an immune response. @clausenlab.bsky.social www.cell.com/cell/fulltex...
cell.com
A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles
Grabarczyk et al. show the structure and mechanism of a non-canonical ubiquitin ligase, which is activated through nucleic-acid-induced oligomerization and is critical for cell survival during immune ...
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Fletcher Lab @fletcherlab.bsky.social · 25/08/2025
Opening for a biochemist to help us in the characterisation of novel ubiquitin-based antivirals. Diverse backgrounds welcomed; a keen sense of adventure is a must 😁 Details and criteria are below; please get in touch with any questions. www.jobs.gla.ac.uk/job/research...
jobs.gla.ac.uk
Research Assistant/Associate
Research Assistant/Associate COLLEGE OF MVLSSchool of Infection & ImmunityResearch and TeachingGRADE 6/7 Job PurposeThe post holder will join the School of Infection & Immunity, MRC-Univers...
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David B. Sauer @davidbsauer.bsky.social · 15/08/2025
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...
nature.com
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...
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Nature Chemical Biology @natchembio.nature.com · 18/08/2025
A new paper reports the structure of the E4 enzyme Ufd2, which mediates K48 branched ubiquitination on K29diUb and K29triUb, identifying Ufd2’s core region as a K29diUb binding domain and a dimeric conformation for distal ubiquitin stabilization www.nature.com/articles/s41...
nature.com
Structural basis for E4 enzyme Ufd2-catalyzed K48/K29 branched ubiquitin chains - Nature Chemical Biology
Tong et al. chemically trapped the structure of the E4 enzyme Ufd2, which mediates K48 branched ubiquitination on K29diUb and K29triUb, identifying Ufd2’s core region as a K29diUb binding domain and a...
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Francis O'Reilly @fjoreilly.bsky.social · 05/08/2025
‼️ Exciting new preprint from a close collaboration with Kylie Walters' group. Our study maps the binding sites of key regulators of the proteasome in situ. www.biorxiv.org/content/10.1...
biorxiv.org
Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy
Proteasome function depends on a network of transient interactions that remain structurally and functionally unresolved. We developed PhIX-MS (Photo-induced In situ Crosslinking-Mass Spectrometry), a ...
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