Timo Denk

Timo Denk

@timodenk.bsky.social

34 followers68 following0 posts

Timo Denk reposted

OMühlemann lab
@omuhlemann-lab.bsky.social

Today, Wojciech Teodorowicz's PhD work on the role of USP9X in occluded A-site RQC was published. Congrats to Wojciech and Lukas, this was not an easy and definitively not a straightforward project. www.cell.com/cell-reports...

cell.comUSP9X promotes the degradation of trapped translation factors on collided ribosomesTeodorowicz et al. show that USP9X, in conjunction with the E3 ligases RNF14 and RNF25, is required to promote the VCP-dependent proteasomal degradation of eRF1 and eEF1A1 trapped in the ribosomal A-site and identify 4EHP as a mediator of translational shutdown following translation factor clearance.

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

Frank Nijpels from VitriMatics paid us a visit today. Not only did he repair our broken VitroBot Mark IV and returned it in person, he also brought some extremely cool tools ❄️ for reliable cryo-EM grid freezing 🔬. Check out the VitriClip and the SupraBlot at vitrimatics.com. #cryoEM #cryoET

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

New preprint! 👀RNAse activity has to be tightly regulated.✂️🧬Here, we present the dynamic architecture of the conserved Rixosome complex – a major player in ribosome maturation and heterochromatin maintenance. Our results give insights into its mode of activation.👇 #cryoEM #Ribosome #RNA

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

Preprint alert: a helicase watching the ribosomal A-site 👀🧬 Our cryo-EM structure reveals how yeast Dhx29 senses mRNA hairpins forming in the A-site and positions its helicase at the mRNA entry channel to resolve them during translation elongation: doi.org/10.64898/202... #cryoEM #ribosome #RNA

Timo Denk reposted

Jean-Paul Armache
@valendraica.bsky.social

We are sharing a tool developed initially for internal use called VOSE (Volume Operations Simplified Edition) today. It is written specifically to work in ChimeraX (version 1.5+), with no additional libraries necessary to be installed. github.com/jparmachelab...

github.comGitHub - jparmachelab/ChimeraX-VOSE: ChimeraX Volume Operations Simplified EditionChimeraX Volume Operations Simplified Edition . Contribute to jparmachelab/ChimeraX-VOSE development by creating an account on GitHub.

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

Proud to share our latest preprint! 🥳 Using a multidisciplinary approach, we uncover a dual function of the snR37 H/ACA snoRNP - combining pseudouridylation with ribosome chaperone activity within a single RNP.🔬🧬 Challenging the traditional view of snoRNP function. 👇 #cryoEM #ribosome #RNA #snoRNA

biorxiv.orgbiorxiv.org

Timo Denk reposted

Ariel Klavaris
@arielchk.bsky.social

Glad to be part of this great work from @beckmannlab.bsky.social, led by @guan316.bsky.social and @timodenk.bsky.social, exploring the mechanics of co-translational acetylation of histones by NAA40.

Dandan GUAN@guan316.bsky.social

Attention handsome people and brilliant minds ！👀🤩 😜🥳Our new paper out in Nature Communications! @natcomms.nature.com @beckmannlab.bsky.social @timodenk.bsky.social @kirmizislab.bsky.social @arielchk.bsky.social #cryoEM#ribosome#translation#histones 🤩Link: www.nature.com/articles/s41...

nature.comNAA40 and NAC cooperate in co-translational histone acetylation in humans - Nature CommunicationsN-terminal histone acetylation by human NAA40 alters epigenetic signaling and affects gene regulation. Here, the authors combine biochemistry and cryo-EM to unravel the foundation for the co-translati...

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

How are histones acetylated as they emerge from the ribosome? We show that NAA40 cooperates with the NAC complex to enable co-translational acetylation of H2A/H4, revealing NAC as a coordinator of nascent protein modification. Read more about our collaboration with @kirmizislab.bsky.social #cryoEM

rdcu.beNAA40 and NAC cooperate in co-translational histone acetylation in humansNature Communications - N-terminal histone acetylation by human NAA40 alters epigenetic signaling and affects gene regulation. Here, the authors combine biochemistry and cryo-EM to unravel the...

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

🎉Thrilled to share that our lab has been awarded an ERC Synergy Grant @erc.europa.eu! Excited for amazing collaborations with the Pertschy (Uni Graz), Henras (CBI Toulouse), and Woodson (Johns Hopkins) labs. #ERCSyG #GeneCenter #LMU #UniGraz #CNRS #JohnsHopkins

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

We are excited to share our collab with @kedrov-lab.bsky.social! Using Cryo-EM❄️ on an amazing sample, we found that YidC is recruited to the back of SecYEG during late-stage substrate insertion —supporting that the "back-of-Sec" route observed in eukaryotes also exists in bacteria 🦠. Check it out👇👇👇

Kedrov Lab @ HHU@kedrov-lab.bsky.social

Very special feelings to announce this one... A project that started like 10 years ago is reaching the finish line, ready to shine. In a dream-team with @beckmannlab.bsky.social we solved the long-chased structure of the active membrane protein insertase SecYEG-YidC www.biorxiv.org/content/10.1...

biorxiv.orgSubstrate-induced assembly and functional mechanism of the bacterial membrane protein insertase SecYEG-YidCThe universally conserved Sec translocon and the YidC/Oxa1-type insertases mediate biogenesis of alpha-helical membrane proteins, but the molecular basis of their cooperation has remained disputed over decades. A recent discovery of a multi-subunit insertase in eukaryotes has raised the question about the architecture of the putative bacterial ortholog SecYEG-YidC and its functional mechanism. Here, we combine cryogenic electron microscopy with cell-free protein synthesis in nanodiscs to visualize biogenesis of the polytopic membrane protein NuoK, the subunit K of NADH-quinone oxidoreductase, that requires both SecYEG and YidC for insertion. We demonstrate that YidC is recruited to the back of the translocon at the late stage of the substrate insertion, in resemblance to the eukaryotic system, and in vivo experiments indicate that the complex assembly is vital for the cells. The nascent chain does not utilize the lateral gate of SecYEG, but enters the lipid membrane at the SecYE-YidC interface, with YidC being the primary insertase. SecYEG-YidC complex promotes folding of the nascent helices at the interface prior their insertion, so the examined cellular pathway follows the fundamental thermodynamic principles of membrane protein folding. Our data provide the first detailed insight on the elusive insertase machinery in the physiologically relevant environment, highlight the importance of the nascent chain for its assembly, and prove the evolutionary conservation of the gate-independent insertion route. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, Ke1879/3, 267205415 (CRC 1208) European Research Council, https://ror.org/0472cxd90, CRYOTRANSLATION

Timo Denk reposted

Beckmann Lab
@beckmannlab.bsky.social

We are happy to share that our snR30 story is finally out in @natureportfolio.nature.com 🥳 We report the first structure of a H/ACA snoRNP acting in ribosome synthesis thereby providing a detailed structural and biochemical view of the snR30 snoRNP guiding local 18S rRNA subdomain folding. 👇👇👇

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