Ján Bíňovský

@worldphageday.bsky.social

🔥My first (co)first-author paper is out🔥 The surfaces of Gram+ and Gram- bacteria are markedly different from each other. How are phages equipped to breach the Gram+ envelope❓ 💡We report a baseplate structure uniquely adapted to infect Gram+ S. aureus. A 🧵⬇️ 1/8 #phagesky #cryoEM 🧪

Ján Bíňovský reposted

World Phage Day

Calling all #PhagePhans and #PhageHunters - wherever you are! It is time for some #PhagePhocus ahead of the 8th #WorldPhageDay and #WorldPhageWeek 2026 - how will you contribute to the 7 day celebration of #AllThingsPhage? #PhageSky @CombatamrOrg on X #AMR #OctoPhage #bacteriophage

Passing this along, because I am genuinely curious about answers.

Alana Cowell 🔬@alanacowell.bsky.social

What do scientists do while in-between positions? How do you handle these gaps? Funding options are limited and getting a position that matches what I want to work on is starting to feel impossible.

23 Sept

Note to self: Do not work late just because of the view! #postdocsky

4 Sept

Phages are weird. Some have T replaced by U in their DNA. In my new role as a #postdoc in Maria Sokolova’s group at the @mpibiochem.bsky.social, I’ll investigate how their transcription machinery recognizes and reads this unusual genome 🧬 1/2

Jeff Lengyel & TEM Team at Thermo Fisher Scientific

4 Sept

If you work on phage transcription, unusual RNA polymerases, or modified nucleic acids, I’d be glad to connect and exchange ideas! #phagesky #Microsky 2/2

Ján Bíňovský reposted

@jefflengyeltemteam.bsky.social

14 July

A beautiful journey through the nuclear pore complex with #cryoET - samples prepared via the Arctis Cryo-Plasma-FIB, data collected with the Glacios Cryo-TEM and segmented in Amira Software. #TeamTomo - See what’s possible with 200 kV cryo-ET: ter.li/n2a8i5po

nature.comWhy paying peer reviewers works, according to a journal’s editor-in-chiefA biology journal that paid peer reviewers found that the approach cut the time to a first editorial decision by 85% and maintained high-quality reviews.

10 July

"Why paying peer reviewers works, according to a journal’s editor-in-chief" I wonder if this is going to change anything.....old idea, new data, uncertain impact. Your thoughts? www.nature.com/articles/d41...

Finally, we propose a mechanism by which the phage 812 initiates its infection. Other contractile-tailed phages infecting Gram+ bacteria likely share such structural features and infection mechanism 💉🦠 7/8

doi.orgConformational changes of the baseplate regulating tail contraction of Staphylococcus phage 812 - The EMBO JournalPhages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10–30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.

Thanks to my colleagues and collaborators🙏 @plevkalab.bsky.social @ceitec.eu And thank you for reading! Let me know if you have any comments or questions. Full story here: doi.org/10.1038/s44318-026-00834-9 8/8

Conformational changes to the baseplate arms cause expansion of the central protein structures, which in turn trigger the tail sheath contraction. 5/8

As the tail sheath contracts, the tail tube is driven toward the host envelope. We detected enzymatic and membrane-interacting domains (and their putative targets) that may facilitate the envelope penetration. 6/8

First of all, we resolved more proteins and domains at the periphery of the native (pre-attachment) baseplate, making a near-complete picture of the whole complex. 3/8

We also got a clearer view of the baseplate in the contracted (post-attachment) state, which only reinforced our previous view of how the baseplate reorganizes its structure: the tripod and RBP proteins reorient, stabilizing the baseplate and anchoring it to the host envelope. 4/8

The manuscript has undergone a major overhaul since 2024. As a result, we determined the baseplate structure of contractile phage 812 in much greater detail. bsky.app/profile/jbin... 2/8

Ján Bíňovský@jbinovsky.bsky.social

Contractile-tailed phages use baseplates to attach to 🦠 and initiate infection. How phages target and penetrate Gram+ 🦠 is poorly understood. Meet phage phi812, a #PhageTherapy contender infecting #AntibioticResistant S. aureus. 2/11

@microbesinfo.bsky.social

19 June

I love when real life issues get explained by science (scientists) so elegantly 👏🏻

Buttons (Ashley) 🏴‍☠️#OFMDForLife🏴‍☠️ 🏳️‍🌈🤡@sevensugars.bsky.social

Since I did do my PhD in cyanobacteria growth and treatment optimization modeling AND work in the water treatment industry, I’m gonna share my theory as to what’s happening here and how to fix it. People are focusing on the painted bottom of the pool increasing residual heat, and while that 1/19

Ján Bíňovský reposted

Microbes.Info

10 Mar

scitechdaily.comStunning High-Resolution Virus Blueprint Offers New Hope Against Antibiotic ResistanceA detailed 3D map of a bacteria-hunting virus reveals ancient origins and new promise against superbugs.

Ján Bíňovský reposted

Aritz Roa-Eguiara

@aritz-roa.bsky.social

7 Mar

🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process. www.biorxiv.org/content/10.6...

19 May 2025

Much needed addition to the AlphaFold Database! 💻 Large potential for use in #StructuralBiology #Phage research.

Gemma C. Atkinson@gemmaatkinson.bsky.social

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

28 Apr 2025

Always happy to provide "wonderfully bad mmCIF files" to make #chimeraX better!

@socialinfluenza.bsky.social

18 Apr 2025

Nice work and awesome #scicomm thread!

Brian Kelch@briankelch.bsky.social

Did you know that there is so much DNA packed inside a phage capsid that the pressure is 10X higher than in a bottle of champagne? In our latest preprint, we wondered how that is contained in a phage that lives at extremely high temperatures. /1 www.biorxiv.org/content/10.1...

Ján Bíňovský reposted

Ed Hutchinson

30 Jan 2025

Our study on pasteurising influenza viruses in milk is now out! It's a nice simple story: influenza viruses (including H5N1) are killed really effectively by pasteurisation, but in raw milk they stay infectious - obvious public health implications of both points... (1/2) rdcu.be/d73te

Ján Bíňovský reposted

Rita Strack

@ritastrack.bsky.social

22 Jan 2025

I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...

pdb101.rcsb.orgPDB101: Molecule of the Month: Assembly Line Polyketide SynthasesLarge multienzyme complexes that synthesize diverse small molecules in a stepwise manner.

13 Jan 2025

I appreciate the stats! Thanks, @pdbeurope.bsky.social for a summary!

Protein Data Bank in Europe (PDBe)@pdbeurope.bsky.social

As we head into 2025, let's take one final look back at 2024 and how the year unfolded in the PDB archive. There were 15319 entries released last year but what more can we find out about those structures ⚖️? A thread 1/11 🧵

Ján Bíňovský reposted

Janet Iwasa

@jiwasa.bsky.social

7 Jan 2025

I'm happy and humbled to take on a new role with @rcsbpdb.bsky.social. I'll be continuing David Goodsell's work on the Molecule of the Month, starting with my first article on Assembly Line Polyketide Synthases! Check it out (animation included!) pdb101.rcsb.org/motm/301

6 Jan 2025

Amazing work and resource! 😍

Ben Engel@cellarchlab.com

Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍 Preprint📜: www.biorxiv.org/content/10.1... A short thread🧵👇

Ján Bíňovský reposted

Fabian Eisenstein

@eisfabian.bsky.social

17 Dec 2024

SPACEtomo v1.2 is online! github.com/eisfabian/SP... - Improved GUIs for lamella detection, target selection and CLEM registration make it the best target selection workflow for PACEtomo on any kind of lamella sample. - Easier installation and configuration Any feedback is much appreciated! :)

17 Dec 2024

🎄Xmas office cleaning 🗑️ ...and how do you organize your thoughts? 🫵 #PhDlife #PhDSky #mindmap

11 Dec 2024

I knew it wouldn't be long before we see #cryoEM structures of a #phage cousin infecting #Archea 🦠 🧪 Beautiful structures from @daumlab.bsky.social, congrats!

The Daum Lab@daumlab.bsky.social

Check out our structure of the archaeal virus HFTV1! Amazing work by two students - Daniel Zhang and Becky Davies, supported by @mathewmclaren.bsky.social. Great collaboration with T. Quax & S. Schwarzer, @hanna-m-oksanen.bsky.social, @the-gold-lab.bsky.social, @misha-isupov.bsky.social & W. Stuart.

22 Nov 2024

Dear #StructuralBiology #PhD #PostDoc peers, join in!

Razvan Borza@rborza.bsky.social

I created this Starter Pack for PhDs and Postdocs in Structural Biology to help connect with colleagues who share similar interests and concerns in the field. Feel free to recommend people or yourself! I'll be adding people 💪🏼😁 bsky.app/starter-pack...

15 Nov 2024

Another useful starter pack 👇

Kate Michie@kmichie.bsky.social

Structural Biology Starterpack go.bsky.app/DDetSBp I like feeds better as it filters out 'cat' talk, leaves in the selective structural biology chitchat (Protein Cosmos). Poke me for inclusion/removal. Apologies if I've broken etiquette and included/excluded you first up (not intended to offend).

14 Nov 2024

In case someone is looking for this...

Rémi Fronzes@fronzeslab.bsky.social

Here is a starter pack for CryoEM/ET enthousiasts To be completed go.bsky.app/JmQksC

bit.lyCell attachment and tail contraction of S. aureus phage phi812bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

8 Nov 2024

Just uploaded a revised version of the manuscript on bioRxiv 🙌 We made some changes to the text and figures, mainly to clarify the naming of proteins. Yeah, it's a challenge to describe things within two different 10MDa structures 🐘

Ján Bíňovský@jbinovsky.bsky.social

🚀Announcing my first (co)first-author manuscript 🚀 "Cell attachment and tail contraction of S. aureus phage phi812" 🔗 bit.ly/Phi812 Explore the structural details of phage interaction with Gram+ bacteria 🤯 #PhageTherapy #cryoEM 🧪 | 🧬🧶 | 🦠 1/11

bit.lyCell attachment and tail contraction of S. aureus phage phi812bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Thanks to my amazing co-first author Marta Šiborová and people from the Plevka Lab for their incredible support 🙌 Special shoutout to all collaborators for their contributions 📈💡 10/11

bit.lyCell attachment and tail contraction of S. aureus phage phi812bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Thanks for reading! If you found this thread interesting, pass it along! bsky.app/profile/jbin... Hopefully, the peer-reviewed version will follow! Also, if you find any mistakes or have suggestions, drop me a ✉️ 11/11

Ján Bíňovský@jbinovsky.bsky.social

bit.lyCell attachment and tail contraction of S. aureus phage phi812bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Changes in the baseplate arms' positions are relayed to the wedge modules and tail sheath initiator proteins, causing their iris-like expansion 👁️ and triggering a gradual tail sheath contraction. This 🌊-like process drives the tail tube through the host cell wall 💉. 8/11

The tail sheath contraction pushes the tail tube's tip into the host cytoplasm, where the genome is ejected 🧬 and infection occurs. Our structural study of phi812 cell wall binding opens up the possibility of designing phi812 to target specific #SAureus strains 🎯 9/11

bit.lyCell attachment and tail contraction of S. aureus phage phi812bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

The central spike protein of phi812 protrudes 22 nm from the baseplate and degrades teichoic acids✂️, enabling the tripod complexes to anchor the phage on the cell wall ⚓️. 6/11

The transformation of tripod complexes frees the hub protein domains to degrade peptidoglycan ✂️ and facilitate penetration of the tail tube through the cell membrane. But how does the tail tube move towards the cell❓ 7/11

bit.lyCell attachment and tail contraction of S. aureus phage phi812bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Upon interaction with the host, the baseplate changes structure, starting with the arms 🦾. These changes include reorienting receptor-binding proteins and tripod complexes that bind to 🦠 via high-avidity interactions with teichoic acids and peptidoglycan. 4/11

The tripod complexes undergo an intra-molecular change. They then “hold hands” together 🤝, stabilizing the post-attachment (contracted) baseplate structure. But how can they reach peptidoglycan covered by teichoic acids❓ 5/11

bit.lyCell attachment and tail contraction of S. aureus phage phi812bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

We used #cryoEM #Xray #NMR #AlphaFold to reconstruct and interpret the phi812 baseplate and tail in detail 🔎. The baseplate of phi812 comprises a core, wedge modules, and baseplate arms that carry receptor-binding proteins 1 & 2 and large tripod complexes. 3/11

rdcu.beEngineering Toxoplasma gondii secretion systems for intracellular delivery of multiple large therapeutic proteins to neuronsNature Microbiology - Toxoplasma gondii secretion systems can be engineered to deliver multiple large therapeutic proteins to neurons in vitro and in vivo.

8 Aug 2024

Reading a lot about contractile phages and injection systems, the idea of leveraging them for cargo delivery always amazed me 🤯 and it's no longer just an idea 🧪 Here, a T. gondii secretion system was hijacked to deliver therapeutic proteins to neurons. Link to study: rdcu.be/dQozB

youtube.comBeyond the Noise #40: Lab leak maniaIn this episode Dr. Offit asks, why did the New York Times publish an op-ed supporting the lab leak theory when all evidence supports a zoonotic spillover?Sh...

31 July 2024

Using MS Word's "Dictate" function these days: "I did an internshit..." "I learned to cry electron microscopy" ...how am I supposed to write a motivation letter with this? 😢

Ján Bíňovský reposted

Kristian G. Andersen

@kgandersen.bsky.social

5 July 2024

Really good 15 min TWiV episode with Paul Offit outlining how false and irresponsible the recent lab leak nonsense from @nytimes.com is. I for one appreciate the brevity - there really is nothing more to it. If you're interested in the topic, give it a listen. www.youtube.com/watch?v=Ukv9...

2 July 2024

Manuscript submitted 🤞 Brace for new structural insights into a bacteriophage landing onto the host cell 🚀

nature.comMeaningfulness in a scientific career is about more than tangible outputsLetter to the Editor

22 Mar 2024

📰 I find myself questioning my scientific career from time to time. This is an encouraging piece. "Meaningfulness in a scientific career is about more than tangible outputs." www.nature.com/articles/d41...