Anuj

New preprint by @alok-bharadwaj.bsky.social explaining the workings of SURFER, a simple tool to segment membrane, micelle or nanodisc densities in cryoEM maps.

Try it via the @chimerax.ucsf.edu ToolShed:

cxtoolshed.rbvi.ucsf.edu/apps/chimera...

Despite LocScale in the name, it works on any map.

Shades of pink we picked for HDCR core 😁 was beautiful!

At long last, the Chlamy chloroplast ribosome hat 🎩 (now renamed the arm 💪) is here to say hello👋! We first spotted this extended structure in green algae a decade ago, and @florentwaltz.bsky.social did beautiful work bringing it into focus! #CryoEM ❄️ #TeamTomo 🔬 #PlantScience 🌾 #ProtistsOnSky 🧪

This is what I call a booster 🚀: Milton and colleagues use a novel, bipyridium-type redox mediator to increase the electrochemical H2 evolution activity of [FeFe]-hydrogenase by a factor of 10 compared to previous protocols.
pubs.acs.org/doi/full/10....

An incredibly challenging single particle cryo-EM structure. Capturing both the N and C termini was difficult enough, but the project required a major effort to resolve the full length protein structure to capture the overall architecture of the KICSTOR-GATOR1 complex.

Well worth it in the end!

I am very excited to share our new preprint - "A Zundel Ion in the Catalytic Proton Transfer Pathway of [FeFe]-Hydrogenase" - for which we revisited an older theory of ours, and came to surprising conclusions... 🧵
doi.org/10.26434/che...

Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...

Our latest work on the nitrogenase-like methylthio-alkane reductase, which specifically reduces reduces carbon-sulfide bonds is now out @natcatal.nature.com: doi.org/10.1038/s419.... We find for the first time large #nitrogenase metalloclusters (P- and L-cluster) outside nitrogenases.

Great work from the lab of @rebeleinlab.bsky.social ! Now out in @natcatal.nature.com

A diagram showing the environmental distribution of methyl coenzyme M reductase encoding Thermoproteota.

New preprint: Methyl co-enzme M reductase encoding (potentially methanogenic) Thermoproteota are widespread and transcriptionally active in diverse anoxic ecosystems! @dr-zj.bsky.social, Matthew Kollom & @emileyeloe-fadrosh.bsky.social www.biorxiv.org/cgi/content/... Funded by the DOE BER program.

Locating the missing chlorophylls f in far-red photosystem I The discovery of chlorophyll f-containing photosystems, with their long-wavelength photochemistry, represented a distinct, low-energy paradigm for oxygenic photosynthesis. Structural studies on chloro...

Have you ever looked at the night sky and wondered if there’s a chlorophyll f in the reaction centre of Photosystem I from far-red light adapted cyanobacteria? 🦠

Well, we did (don’t judge) and the work that followed is now out as a First Release in @science.org

www.science.org/doi/10.1126/...

Cryo-EM structure of Chlamydomonas Photosystem I complexedwith the alternative electron donor cytochrome c6 www.biorxiv.org/content/10.1101/2025.09.08.674899v1 #cryoEM

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).

A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.

Happy to share that our story on the bacterial archaellum was published today in @natmicrobiol.nature.com
www.nature.com/articles/s41...

Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social

This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

Congrats Hannah Ochner and authors on this important paper! Strong collaboration with @kiranrpatil.bsky.social

www.biorxiv.org/cgi/content/...
@mrclmb.bsky.social @wellcometrust.bsky.social

It is out now 🥳🥂
I am very happy to be part of this nice collaboration in which we were able to characterize different bacterial chemoreceptors and their ligand specificities. Amazing teamwork with Wenhao Xu, the Sourjik lab, @bangebalcony.bsky.social, et. al 🤩

👇👇👇
www.pnas.org/doi/10.1073/...

The Role of Selenocysteine in Catalysis and Oxygen Tolerance of a W-Dependent Formate Dehydrogenase Metal-dependent formate dehydrogenases (FDHs) catalyze, under mild conditions, the reversible reduction of CO2 to formate, a versatile C1 feedstock that can contribute to a carbon-neutral economy. Metal-dependent FDHs are the most widespread selenoproteins found in bacteria, and around 44% of them include selenocysteine (Sec) as a ligand to the Mo/W active site. In the sulfate-reducer Nitratidesulfovibrio vulgaris Hildenborough, the main FDH responsible for CO2 reduction is the W/Sec-dependent FdhAB, which is among the most active CO2 reductases reported so far. In contrast to most metal-dependent FDHs, this enzyme is relatively O2-tolerant and can be purified aerobically. In this work, we evaluated the role of Sec in the catalytic and stability properties of the W/Sec-FdhAB. For that, a Sec-to-Cys variant (U192C) was created, its catalytic and spectroscopic properties were characterized, and its crystal structure was determined. Sec substitution by Cys strongly affects activity, decreases the KM for formate, and increases susceptibility to O2. While Sec-to-Cys replacement induces only weak changes of the WV EPR signals, using 77Se-labeled enzyme, we could show that Sec undoubtedly coordinates the W metal in the WV redox state. The crystal structure of U192C confirmed previous findings on the redox switch mechanism of activation and protection of FdhAB, while revealing a putative catalytic intermediate of FdhAB with Arg441 orienting a CO2 substrate analog (probably SO2) in the active site. Overall, the results indicate that Sec plays a critical role in the high activity displayed by W/Sec-FdhAB, and that it may also be involved in or modulate the proton transfer to and from the active site.

Very excited about this story: Inês Pereira et al. reveal the role of selenocysteine in catalysis and O2-tolerance of a tungsten-dependent formate dehydrogenase (via ACS Catalysis)
doi.org/10.1021/acsc...

Proud to see our work on metalloenzymes - and methyl coenzyme M reductase (MCR) in particular - featured in the print version of Berlin's @tagesspiegel.de 🤩
⛓️ www.uni-potsdam.de/fileadmin/pr...

Atomic-resolution structure of a chimeric Powassan tick-borne flavivirus The 2.8-Å resolution structure is presented for a chimeric construct of an emerging tick-borne flavivirus, Powassan virus.

New in @science.org
We built a safe, atomic-resolution version of the Powassan virus—a deadly tick-borne #flavivirus with no vaccine.
✅ First structure ever
✅ Safe to handle (BSL-2)
✅ Platform for vaccines & antivirals

Let me show you 🧵 (1/5)

Link: www.science.org/doi/10.1126/...

Our new preprint: how photoprotection is spatially coordinated with energy metabolism. Photosystem I is major source of radicals. We report EM structure of PSI in complex with superoxide dismutase SOD: direct link between energy conversion & oxidative stress defence
www.biorxiv.org/content/10.1...

Our new consensus statement on reducing and reporting contamination in microbiome studies is the cover image of this month's Nature Microbiology: www.nature.com/articles/s41... In the cover photo, you can see our postdoc Sophie Holland in fully PPE sampling the atmosphere of terrestrial Antarctica.

Electron flow in hydrogenotrophic methanogens under nickel limitation - Nature Two distantly related methanogens shift the methanogenic pathway under nickel limitation, suggesting that methanogens adapt to changing bioavailability of nickel by rerouting electron flow between two...

Our new study shows how nickel limitation changes electron flow in methanogens.
@nature.com
#methanogens #methane #archaea
www.nature.com/articles/s41...

Happy to share Yiting's new paper on artificial micro hydrogenase aka... Ferredoxin⁉️
Out now in Advanced Science doi.org/10.1002/advs...

Our ferredoxin story @chemicalscience.rsc.org now in print, just in time for my presentation tomorrow #ISABC17 👏🏻
Sahin et al., Chem. Sci., 2025, 16, 10465-10475
pubs.rsc.org/en/content/a...

Excellent work from my dear friend Sriram! Many congratulations @georghochberg.bsky.social !

Excellent work from my colleagues Tristan and Eva on the structure of the ancient sodium pumping Mtr complex from methanogens! Happy to contribute alongside @tomaspascoa.bsky.social @ezimmer.bsky.social @schullerjm.bsky.social

Clustering for methane - Nature Catalysis Nature Catalysis - Clustering for methane

CLUSTERING FOR METHANE
Nice write-up @natcatal.nature.com of our recent article on MCR activation 🙏🏻
www.nature.com/articles/s41...

Two Key Ferredoxins for Nitrogen Fixation Have Different Specificities and Biophysical Properties Two ferredoxins, FdC and FdN, are collectively essential for the process of nitrogen fixation by the iron nitrogenase in R. capsulatus. We explore the biophysical factors, through spectroscopic and s....

Leveraging spectroscopic and structural approaches we obtained new insights into the role of #ferredoxins in N2 fixation. Just published in Chemistry – A European Journal: doi.org/10.1002/chem...! Great work by Holly Addison. Fantastic collaboration with Antonio Pierik on the EPR characterization.

Interesting thread 🧵 from @georghochberg.bsky.social dissecting the evolution of nitrogenases from cofactors of methane-producing enzymes. The “molecular paleontology” possible with modern technology is so cool. 🧪🧶🧬