Dan Grabarczyk
@dangrabarczyk.bsky.social
Structural biologist - currently ubiquitin ligases, previously DNA replication and bacterial metabolism
Research Associate - Clausen Lab, IMP Vienna
Research Associate - Clausen Lab, IMP Vienna
Reposted by Dan Grabarczyk
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
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...
rdcu.be
November 17, 2025 at 11:37 AM
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Reposted by Dan Grabarczyk
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...
www.nature.com/articles/s41...
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-...
www.nature.com
November 14, 2025 at 8:51 PM
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...
www.nature.com/articles/s41...
Reposted by Dan Grabarczyk
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...
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...
November 7, 2025 at 10:44 AM
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...
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...
Reposted by Dan Grabarczyk
📢 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
October 31, 2025 at 9:24 AM
📢 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
Reposted by Dan Grabarczyk
Split-site ubiquitination gives ZNFX1 new power in RNA defense @cellcellpress.bsky.social
www.cell.com/molecular-ce...
www.sciencedirect.com/science/arti...
www.cell.com/molecular-ce...
www.sciencedirect.com/science/arti...
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...
www.cell.com
October 17, 2025 at 4:37 PM
Split-site ubiquitination gives ZNFX1 new power in RNA defense @cellcellpress.bsky.social
www.cell.com/molecular-ce...
www.sciencedirect.com/science/arti...
www.cell.com/molecular-ce...
www.sciencedirect.com/science/arti...
Reposted by Dan Grabarczyk
Elaborate machinery for inserting proteins into the outer membrane of bacteria www.nature.com/articles/d41...
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.
www.nature.com
October 2, 2025 at 9:29 AM
Elaborate machinery for inserting proteins into the outer membrane of bacteria www.nature.com/articles/d41...
Reposted by Dan Grabarczyk
Structure and substrate recognition by the Twin-arginine translocation (Tat) pathway core complex https://www.biorxiv.org/content/10.1101/2025.09.18.677151v1
September 19, 2025 at 3:46 AM
Structure and substrate recognition by the Twin-arginine translocation (Tat) pathway core complex https://www.biorxiv.org/content/10.1101/2025.09.18.677151v1
Thanks a lot to Yiyun Song @natchembio.nature.com for highlighting our ZNFX1 paper. www.nature.com/articles/s41...
Dimerization for activation - Nature Chemical Biology
Nature Chemical Biology - Dimerization for activation
www.nature.com
September 27, 2025 at 1:52 PM
Thanks a lot to Yiyun Song @natchembio.nature.com for highlighting our ZNFX1 paper. www.nature.com/articles/s41...
Reposted by Dan Grabarczyk
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 🧬🧪
September 23, 2025 at 5:08 PM
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 🧬🧪
Reposted by Dan Grabarczyk
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...
More info: www.imb.de/students-pos...
Laura Lorenzo Orts
IMB Mainz
www.imb.de
September 15, 2025 at 12:13 PM
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...
More info: www.imb.de/students-pos...
Reposted by Dan Grabarczyk
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...
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...
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...
www.biorxiv.org
September 8, 2025 at 1:53 PM
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...
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...
Reposted by Dan Grabarczyk
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/...
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...
www.imp.ac.at
August 28, 2025 at 6:28 PM
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/...
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/...
August 28, 2025 at 6:54 PM
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/...
Reposted by Dan Grabarczyk
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...
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...
www.imp.ac.at
August 28, 2025 at 7:33 AM
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...
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...
www.cell.com/cell/fulltex...
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 ...
www.cell.com
August 27, 2025 at 7:04 PM
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...
www.cell.com/cell/fulltex...
Reposted by Dan Grabarczyk
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...
Details and criteria are below; please get in touch with any questions.
www.jobs.gla.ac.uk/job/research...
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...
www.jobs.gla.ac.uk
August 25, 2025 at 12:34 PM
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...
Details and criteria are below; please get in touch with any questions.
www.jobs.gla.ac.uk/job/research...
Reposted by Dan Grabarczyk
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...
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
August 15, 2025 at 10:00 AM
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...
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...
Reposted by Dan Grabarczyk
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...
www.nature.com/articles/s41...
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...
www.nature.com
August 18, 2025 at 4:44 PM
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...
www.nature.com/articles/s41...
Reposted by Dan Grabarczyk
‼️ 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...
www.biorxiv.org/content/10.1...
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 ...
www.biorxiv.org
August 5, 2025 at 4:21 PM
‼️ 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...
www.biorxiv.org/content/10.1...
Reposted by Dan Grabarczyk
New preprint: In situ Architecture of #Plasmodesmata.
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
July 26, 2025 at 3:38 PM
New preprint: In situ Architecture of #Plasmodesmata.
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Reposted by Dan Grabarczyk
🎉 Congratulations to our Daniel Grabarczyk, research associate in the Clausen lab, who has been awarded a prestigious FWF Principal Investigator Project Grant to support his research into the molecular mechanisms of innate immunity against viruses.
Read more: www.imp.ac.at/news/article...
Read more: www.imp.ac.at/news/article...
July 9, 2025 at 8:54 AM
🎉 Congratulations to our Daniel Grabarczyk, research associate in the Clausen lab, who has been awarded a prestigious FWF Principal Investigator Project Grant to support his research into the molecular mechanisms of innate immunity against viruses.
Read more: www.imp.ac.at/news/article...
Read more: www.imp.ac.at/news/article...
Reposted by Dan Grabarczyk
This is just an excellent preprint by Rasmus Jensen and colleagues from Julia Mahamid's lab @embl.org - a tour de force of Cryogenic electron tomography to do in cell structural biology in which they discover a new complex and solve its structure and function! www.biorxiv.org/content/10.1...
In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex
Cryo-electron tomography has emerged as powerful technology for in-cell structural biology, and in combination with breakthroughs in protein structure prediction, offers a unique opportunity for illum...
www.biorxiv.org
May 22, 2025 at 7:01 PM
This is just an excellent preprint by Rasmus Jensen and colleagues from Julia Mahamid's lab @embl.org - a tour de force of Cryogenic electron tomography to do in cell structural biology in which they discover a new complex and solve its structure and function! www.biorxiv.org/content/10.1...
Reposted by Dan Grabarczyk
Great to see this out. A story that spanned continents, cities and budget codes…
www.nature.com/articles/s41...
Big thanks to all the teams involved!
@clausenlab.bsky.social @e3chembio.bsky.social
www.nature.com/articles/s41...
Big thanks to all the teams involved!
@clausenlab.bsky.social @e3chembio.bsky.social
ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213 - Nature Communications
RNF213 is an E3 ligase with ATPase activity. Here, the authors show that RNF213 is activated by ATP binding and senses cellular energy states, and reveal a transthiolation mechanism induced by immune ...
www.nature.com
May 13, 2025 at 9:51 AM
Great to see this out. A story that spanned continents, cities and budget codes…
www.nature.com/articles/s41...
Big thanks to all the teams involved!
@clausenlab.bsky.social @e3chembio.bsky.social
www.nature.com/articles/s41...
Big thanks to all the teams involved!
@clausenlab.bsky.social @e3chembio.bsky.social
Amazing chemical biology/structural biology work on K29/K48 branching E3 Ufd4/TRIP12 www.nature.com/articles/s41...
Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination - Nature Communications
The K29/K48 hetero-polyubiquitin signal has been reported to be an enhanced degradation signal, but the enzymatic mechanism of this ubiquitin chain formation is unclear. Here, the authors reveal how t...
www.nature.com
May 10, 2025 at 12:05 PM
Amazing chemical biology/structural biology work on K29/K48 branching E3 Ufd4/TRIP12 www.nature.com/articles/s41...