Lightnews — Scholar-powered news

Reposted by Luigi Scietti

The Rosalind Franklin Institute @rosfrankinst.bsky.social · Aug 18

Exciting work from the Franklin, @ox.ac.uk, and @diamondlightsource.bsky.social has led to a new method for imaging small proteins (<50 kDa) using cryoEM. By using bifunctional, bispecific nanobody scaffolds, the team have successfully solved the smallest protein structure to date (14 kDa).

Quote from Dr. Mingda Ye, University of Oxford, highlighting the collaborative breakthrough in cryo-EM imaging of small proteins: “This idea was initiated when solving sub-50kDa protein structures by cryo-EM was almost impossible. To break this barrier, many world-class scientists in different fields have combined forces and it is a great honour to work with them to bring this game-changing tool into reality!” The background diagram outlines the scientific workflow used in the study.

1 8 13

Reposted by Luigi Scietti

Manchester Cell Matrix Centre @mcrcellmatrix.bsky.social · Aug 15

Amazing new paper from Clair Baldock's lab resolves the collagen VI microfibril structure by cryo-EM to reveal a cysteine-rich coiled-coil crucial for heterotrimerization & microfibril assembly. The structure also reveals a hotspot of collagen VI muscular dystrophy mutations that disrupt assembly.

Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations

Nature Communications - Collagen VI microfibril cryo-EM structure resolves a cysteine-rich coiled-coil important for heterotrimerization and microfibril assembly, reveals a hotspot of collagen VI...

rdcu.be

1 2

Reposted by Luigi Scietti

Martin Pacesa @martinpacesa.bsky.social · Jun 30

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!

github.com/martinpacesa...

4 55 140

Reposted by Luigi Scietti

Yehlin Cho @yehlincho.bsky.social · Jun 3

🚀 Excited to release BoltzDesign1!

✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌

🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social

1 17 54

Reposted by Luigi Scietti

Jean-Paul Armache @valendraica.bsky.social · May 30

New collaborative paper between JPArmache and Bowman (@bowmanlab-jhu.bsky.social) labs show how the yeast CHD1 chromatin remodeler depends on activator elements to distort nucleosomal DNA. This explains how the NegC inhibitor blocks activity. www.nature.com/articles/s41...

A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA - Nature Structural & Molecular Biology

Nodelman, Folkwein et al. define a regulatory region in Chd1 containing adjacent inhibitor and activator elements that compete for binding to the remodeler ATPase. The competition between these elemen...

www.nature.com

2 4 14

Reposted by Luigi Scietti

Kevin Drew @ksdrew.bsky.social · May 29

Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes.

www.embopress.org/doi/full/10....

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments | Molecular Systems Biology

imageimagehu.MAP3.0 integrates mass spectrometry experiments to identify human protein complexes. Using this resource, this study characterizes covariation of complexes, identifies mutually exclusive ...

www.embopress.org

3 28 53

Luigi Scietti @luigiscietti.bsky.social · May 28

Amazing #cryoEM structures and incredible community here at @cniostopcancer.bsky.social for the “machines acting on DNA and RNA” congress!

2 11

Luigi Scietti @luigiscietti.bsky.social · Apr 22

I also had fun in making gummy GLT25D1 making #notthecover using #blender

1 3

Luigi Scietti @luigiscietti.bsky.social · Apr 22

This was a massive work from @fornerislab.bsky.social fellows to ehihc I contributed when I was Postdoc, and great #teamwork with Giorgio Colombo lab, @claudio-iacobucci.bsky.social and Alberta Pinnola lab.

1 1 1

Luigi Scietti @luigiscietti.bsky.social · Apr 22

we found that the GT1 domain, while not catalytic, is surprisingly capable of binding Ca²⁺ and UDP-α-galactose. This was intriguing to us, but all the mutants in the GT1 site did not produce folded protein, consistent with a structural role for the GT1 (also confirmed by MD).

1

Luigi Scietti @luigiscietti.bsky.social · Apr 22

And here the question: are they both active? which one is the responsible for the GalT activity? We combined #mutagenesis with #biophysics and #moleculardynamics to show that only the GT2 domain exhibits catalytic activity, facilitated by an unusual Glu-Asp-Asp motif critical for Mn²⁺ binding.

2 1 1

Luigi Scietti @luigiscietti.bsky.social · Apr 22

Each monomer contains two domains (GT1 and GT2) connected by a long but ordered linker. Surprisingly, both domains are capable of binding metal ions and the donor substrate UDP-α-galactose.

1

Luigi Scietti @luigiscietti.bsky.social · Apr 22

We solved the #Xray structure of GLT25D1/COLGALT1 via experimental phasing (yes, it was before #Alphafold) showing that it forms an elongated head-to-head homodimer

1 1

Luigi Scietti @luigiscietti.bsky.social · Apr 22

Collagen's function are ensured by essential post-translational modifications including galactosylation.
GLT25D1 is the galactosyltransferase enzyme responsible for initiating the glycosylation of hydroxylysine in collagen. but its structure was missing until now

1

Luigi Scietti @luigiscietti.bsky.social · Apr 22

Super happy to share the final shape of our work describing the molecular #structure and #enzymatic mechanism of human #collagen #galactosyltransferase #GLT25D1 published in @natcomms.nature.com. Want to know how collagen become sweet? read the 🧵 below!

Forneris Lab @UniPV @fornerislab.bsky.social · Apr 16

Excited to share our new Nature Communications paper describing the molecular structure and the biochemical characterization of human #collagen #galactosyltransferase GLT25D1/COLGALT1 #glycotime www.nature.com/articles/s41...

Molecular structure and enzymatic mechanism of the human collagen hydroxylysine galactosyltransferase GLT25D1/COLGALT1 - Nature Communications

Hydroxylysine galactosylation is essential for collagen maturation. This work reveals the molecular structure of human GLT25D1, its catalytic residues, and a noncatalytic structural domain stabilized ...

www.nature.com

1 1 4

Reposted by Luigi Scietti

Kat Toropova @kattoropova.bsky.social · Mar 18

We are thrilled to announce the 2025 EMBO practical course in cryo-em image processing, Birkbeck College, London, 9-16 Sept 2025. More info & apply: meetings.embo.org/event/25-cry... Organisers Giulia Zanetti & Helen Saibil. Beautiful image from co-organizer @carolynmoores1.bsky.social lab.

Image processing for cryo-electron microscopy

Cryo electron microscopy (cryo EM) is a major structural biology method for studying macromolecular complexes and cellular structures in their native states. Stable high resolution cryo microscopes, …

meetings.embo.org

1 18 31

Reposted by Luigi Scietti

Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · Mar 4

This is a masterpiece ! #cryoEM

Structures of H2A.Z-associated human chromatin remodelers SRCAP and TIP60 reveal divergent mechanisms of chromatin engagement

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

3 20

Reposted by Luigi Scietti

NanoImaging Services @nanoimaging.bsky.social · Mar 4

Did you make our cryo-EM webinar last week? Dive into pre-processing, how to interpret 2D classes, 3D reconstructions from the initial map to final structure with CSO Giovanna Scapin.

Catch it here: youtu.be/2dBnPVkaoFs

Sign up for Overcoming Limitations, on 3/25: nimgs.zoom.us/webinar/regi...

1 4

Reposted by Luigi Scietti

Lorna Malone @drlornamalone.bsky.social · Feb 18

📢 Registration is now open for 'Wellcome-MRC Cryo-EM in Structural Biology 2025'!

📅 Join us online March 3-7 at @diamondlightsource.bsky.social @universityofleeds.bsky.social for lectures & demos in #CryoEM & #CryoET: sample prep, SPA, model building & more!🧬

🔗 www.diamond.ac.uk/Instruments/...

Wellcome-MRC Cryogenic Electron Microscopy in Structural Biology 2025 - - Diamond Light Source

eBIC (Diamond light source) has partnered with the Astbury Biostructure Lab (University of Leeds), the Scottish Centre for Macromolecular Imaging (University of Glasgow), Midlands Regional Cryo-EM Fac...

www.diamond.ac.uk

9 16

Reposted by Luigi Scietti

Bird account @dialecticbio.bsky.social · Mar 3

Been thinking about creating a collection of good protein structure figures, as inspiration for my own work.

#1 www.nature.com/articles/s41...

7 54 170

Reposted by Luigi Scietti

Greg Chojnowski @gchojnowski.bsky.social · Feb 6

I’m happy to share gapTrick, an AlphaFold2-based tool for characterising protein-protein complexes

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

gapTrick - Structural characterisation of protein-protein interactions using AlphaFold with multimeric templates

The structural characterisation of protein-protein interactions is a key step in understanding the functions of living cells. Models of protein complexes provide important insights into interaction me...

www.biorxiv.org

1 3 5

Reposted by Luigi Scietti

Carlos Moreno-Yruela @carlosmyruela.bsky.social · Feb 4

#SIRT7 is a histone deacetylase with highly specific activity on #chromatin substrates.
We just published mechanism-based #cryoEM structures of #SIRT7 on nucleosomes to understand its activity 👇
www.nature.com/articles/s41...
(1/8) #ChemBio #ChemSky

1 17 43

Luigi Scietti @luigiscietti.bsky.social · Jan 29

Cool event, great people! Thanks for putting us together @fornerislab.bsky.social and @thermofishersci.bsky.social!

Forneris Lab @UniPV @fornerislab.bsky.social · Jan 29

The lecture room is really packed for this @thermofishersci.bsky.social #cryoem roadshow in Pavia today!

1

Reposted by Luigi Scietti

Jan Huertas @janhuemar.bsky.social · Jan 22

Exciting new preprint alert! 🚨 The Collepardo lab, teaming up with Huabin Zhou and the Rosen lab we took a deep, high-resolution look into chromatin condensates! [1/6] #Chromatin #MD @rcollepardo.bsky.social @juliamaristany.bsky.social
www.biorxiv.org/content/10.1...

www.biorxiv.org

1 12 37

Luigi Scietti @luigiscietti.bsky.social · Jan 14

Truly honoured to be the first user of such an amazing platform! For sure a reference point for all the Italian community. Exciting time ahead! ❄️🚀

Paolo Swuec @pscryoem.bsky.social · Jan 13

A real milestone for the local community, today we celebrate the beginning of service provision by @humantechnopole.bsky.social National Facility for Structural Biology. Lucky to have a smiling @luigiscietti.bsky.social (in pic with our Gaetano D'Urso) from IEO as first user to the Cryo-EM Unit.

6