Yoshi Ichikawa

The small #GTPase Rab1 is a master regulator of #Golgi traffic and #autophagy. van Vliet, Munro et al. @mrclmb.bsky.social performed a proteomic screen to identify novel Rab1 effectors, including a #dynein motor adaptor and cargo receptors for autophagy. rupress.org/jcb/article/...

#Trafficking

#KANK1 #LC8 #IntrinsicallyDisorderedProteins #AlphaFold #EM

Disordered linker of Kank1 forms rigid protein rod upon binding to 15 LC8 molecules and bridge the gap between membrane and microtubule.

New collaborative preprint!
A striking result: a disordered linker in KANK1 binds as many as 15 LC8 dimers, forming a protein rod that bridges cell membranes and microtubules!
www.biorxiv.org/content/10.1...

Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social

Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.

Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET

Weak Motifs, Strong Complex: KANK1 Uses Cooperative Multivalency with the Hub-Protein LC8 to Bridge Cytoskeletal Complexes https://www.biorxiv.org/content/10.1101/2025.07.16.665182v1

New Online! Critical constituents and assembly principles of centriole biogenesis in human cells

Dynein-2 prefers to bind the retrograde-targeted A-tubule in intraflagellar transport - likely because of its tyrosination, suggest cryo-ET data and MD simulations by @ichikawa-lab.bsky.social and coworkers
www.embopress.org/doi/full/10....

Cryo-ET and MD simulations reveal that dynein-2 is tuned for binding to the A-tubule of the ciliary doublet | The EMBO Journal imageimageDynein-2 is a motor protein essential for retrograde intraflagellar transport (IFT) on the A-tubule of ciliary doublet microtubules. Here, biochemical and cryo-ET analyses demonstrate that d...

Our paper on dynein-2's track recognition mechanism is now published in The EMBO Journal @embojournal.org!!

Cryo-ET and MD simulations reveal that dynein-2 is tuned for binding to the A-tubule of the ciliary doublet | The EMBO Journal www.embopress.org/doi/full/10....

Volume 138 Issue 20 | Journal of Cell Science | The Company of Biologists Journal of Cell Science publishes cutting-edge science encompassing all aspects of cell biology. It is published by The Company of Biologists, a not-for-profit organisation.

Our special issue on ‘Cilia and Flagella’ is now out! Huge thanks to all (authors + reviewers) who contributed, and to our wonderful Guest Editors (@cilialab.bsky.social + @lottepedersen.bsky.social) for pulling it together.
Happy reading!
#cilia #flagella

journals.biologists.com/jcs/issue/13...

Advances in ciliary proteomics – towards cracking the hidden proteome code of cilia Summary: This Review explores proteomic strategies for investigating cilia, tracing the evolution from early discoveries to recent advancements enabled by proximity labeling techniques.

📣 Here it is — our overview on ciliary proteomics! Great discussions and writing with @mick-lab.bsky.social and Ronald Roepman 🙏🙏
Hope we didn’t miss anything important - apologies if we did!

#cilia #ciliopathies #proteomics
@theracilproject.bsky.social @for5547.bsky.social

tinyurl.com/yc8ztn5v

a man stands in front of a white board with the words keep that in mind written on it ALT: a man stands in front of a white board with the words keep that in mind written on it

Miao Gui and I wrote a Review for the @jcellsci.bsky.social special issue “Cilia and Flagella: From Basic Biology to Disease”. It provides a comprehensive and up-to-date overview of MIP structure, function, and the latest tools used to study them, crafted to serve both newcomers and experts.

Microtubule inner proteins – bridging structure and function in ciliary biology Summary: Microtubule inner proteins (MIPs) have been brought into focus by the cryo-EM revolution. This Review outlines current knowledge, emerging functions, links to ciliopathies and outstanding que...

Ever wondered what microtubule inner proteins (MIPs) are and what they actually do? Or perhaps you already know about them, but find it hard to keep track of which ones are conserved across species and how they support ciliary structure and function?
journals.biologists.com/jcs/article/...

1000 citation alert by Google Scholar

A milestone reached! 1000 citations on Google Scholar!

Molecular basis for the activation of outer dynein arms in cilia Nature Structural & Molecular Biology, Published online: 29 September 2025; doi:10.1038/s41594-025-01680-9Issa et al. show that the ciliary small guanosine triphosphatase Arl3 displaces the inhibitory regulator Shulin/DNAAF9 from the outer dynein arm, leading to motor activation.

New online: Molecular basis for the activation of outer dynein arms in cilia

SUN5 forms a regular protein lattice reinforcing the sperm head-tail junction Linker of nucleo- and cytoskeleton (LINC) complexes reside in the nuclear envelope, the double-membrane surrounding the nucleus, where they establish a physical bridge between nucleus and cytoplasm. L...

I am happy our recent study on the human sperm head-tail junction is now online. We find that SUN5 form an hexagonal lattice at the nuclear membrane, rationalising how mutations in SUN5 lead to infertility. Great work of @cryonas.bsky.social !
www.biorxiv.org/content/10.1...

Happy to share our lab's recent #cryoEM studies that show how a SPIN90 dimer activates Arp2/3 complex to form either uni or bidirectional actin filaments. Congrats🎉👏 @justusfrancis.bsky.social @achyutha-kp.bsky.social @tejashyamk.bsky.social @sridharskulkarni.bsky.social @kiranvyshnav.bsky.social

Excited to share our latest work with @simonbullock11.bsky.social! We looked at how diverse mRNAs get selected for subcellular localization and it turns out that a single protein can recognize different RNA elements using shared features that weren’t apparent before.
www.biorxiv.org/content/10.1...

Thrilled to see our study on how kinesin-2 motors are switched on and off published in @natsmb.nature.com ⚛️

➡️ www.nature.com/articles/s41...

Congrats to all authors from me and Anthony 🎉 @dunnschool.bsky.social Check out this animation made by talented PhD student @matthew-batisio.bsky.social 😆

Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1 - Nature Chemical Biology Cryo-electron microscopy and biochemical reconstitution analysis reveals that Nde1 enhances Lis1 binding to autoinhibited dynein, promoting formation of a Phi-like–Lis1 intermediate during dynein acti...

Cryo-EM and biochemical reconstitution analysis reveal that Nde1 enhances Lis1 binding to autoinhibited dynein, promoting formation of a Phi-like-Lis1 intermediate during dynein activation

www.nature.com/articles/s41...

Associate or Senior Editor, Nature Biomedical Engineering Job Title: Associate or Senior Editor, Nature Biomedical Engineering Organization: Nature Portfolio Location: New York, Jersey City, Shanghai or Beijing – Hybrid Working Closing date: August 20, 2025 ...

If you’d like to join me on this journey, NBME is hiring!! This is a fantastically rewarding career that keeps you very much in science. springernature.wd3.myworkdayjobs.com/SpringerNatu...

Associate Editor or Senior Editor, Nature Methods Title: Associate or Senior Editor, Nature Methods Organization: Nature Portfolio Locations: New York, Jersey City, Shanghai or Beijing Closing Date: August 3, 2025    About Springer Nature Springer Na...

Nature Methods is also hiring to replace me (applications close August 4th!!!) and I will do everything I can to support their next bioimaging editor (ask me anything!). springernature.wd3.myworkdayjobs.com/SpringerNatu...

Congratulations!!! 🎉🎉🎉

Forces in Cell Biology Cell generate forces to maintain normal tissue morphology and function. Cells can also sense and process forces appropriate to their correct tissue context. ...

🚨Last call to submit to the Forces in Cell Biology collection with @natcomms.nature.com and Scientific Reports! Deadline: 24th July

www.nature.com/collections/...

Come work at Nature Methods! A dream job. I know from experience 😄

New preprint from the lab - the first paper made (almost) entirely here @qmul.bsky.social

We report how human outer kinetochore complexes Ndc80 and Ska form cooperative oligomers, that together stabilise microtubule ends against shortening.
www.biorxiv.org/content/10.1...

Key results below: (1/7)

The Mn-motif protein MAP6d1 assembles ciliary doublet microtubules - Nature Communications Cilia are composed of microtubule doublets, but how they assemble is unclear. Here, the authors show that the brain-specific MAP6d1, found in neuronal primary cilia, assembles doublet microtubules and...

Another method to reconstitute doublet microtubules by Gopal et al.!
www.nature.com/articles/s41...

Latest preprint from the lab, many years in the making!

By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase.

This could have big implications for our understanding of viral replication & assembly (🧵)

www.biorxiv.org/content/10.1...

Daniel's paper is now published in @jcellsci.bsky.social, great experience with @reviewcommons.org 😀

Want to know everything tubulin assembly in trypanosome flagella and other microtubules? Here is the link:

journals.biologists.com/jcs/article/...

Unveiling the structural spectrum of SARS-CoV-2 fusion by in situ cryo-ET | Nature Communications SARS-CoV-2 entry into host cells is mediated by the spike protein, which drives membrane fusion. While cryo-EM reveals stable prefusion and postfusion conformations of the spike, the transient fusion intermediate states during the fusion process remain poorly understood. Here, we design a near-native viral fusion system that recapitulates SARS-CoV-2 entry and use cryo-electron tomography (cryo-ET) to capture fusion intermediates leading to complete fusion. The spike protein undergoes extensive structural rearrangements, progressing through extended, partially folded, and fully folded intermediates prior to fusion-pore formation, a process that depends on protease cleavage and is inhibited by the WS6 S2 antibody. Upon interaction with ACE2 receptor dimer, spikes cluster at membrane interfaces and following S2’ cleavage concurrently transition to postfusion conformations encircling the hemifusion and initial fusion pores in a distinct conical arrangement. S2’ cleavage is indispensable fo

SARS-CoV-2 entry captured: Cryo-ET reveals fusion intermediates of spike protein during membrane fusion, bridging stable pre- and postfusion states. PMID:40461447, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-60406-z #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

🇨🇦🚨Job Alert🚨🇨🇦
Canada Excellence Research Chair (C$5 or C$10M, 8 yr budget)
U Toronto, Dept of Biochem/LabMedPath
*Was just told they're looking for a structural biologist using cryoEM* (related to infectious disease?)
Are you an established PI ready to move to 🇨🇦?
research.utoronto.ca/funding-oppo...