Yang Lee

Looking forward to the Grand Opening of the Northern Eye Imaging facility on 5th November at the Frederick Douglass Centre, Newcastle. Register now nusbf.ncl.ac.uk/ccpem-tfs-ne... for the latest #structuralbiology and #cryoem in the region, to see the new Tundra cryo-TEM and lots more!

Rescaling FSC curves pubmed.ncbi.nlm.nih.gov/41059947/ #cryoEM

Below (by @landerlab.bsky.social) is the 2nd #cryosparc recipe on @biorxivpreprint.bsky.social in a month. I remain worried about closed-source software affecting progress in #cryoEM. We should develop new algorithms instead!

#OpenSoftwareAcceleratesScience

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

Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoEM

Confidence-guided cryo-EM map optimisation with LocScale-2.0 www.biorxiv.org/content/10.1101/2025.09.11.674726v1 #cryoEM

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

Magellon has taken off to explore your cryo-EM data! Now out in @iucrj.iucr.org doi.org/10.1107/S205... Congrats to all involved!

At Darwin College: Richard Henderson Jacqueline Milne Sriram Subramanian Nigel Unwin David Barford Da-neng Wang John Rubinstein

John ring's the LMB seminar bell to call the audience back in after a coffee break.

Returned from a wonderful symposium in honour of the 50th anniversary of Richard Henderson's and Nigel Unwin's 1975 paper on the structure of bacteriorhodopsin - the paper that started the field of membrane protein structural biology.
Also fulfilled my dream of ringing the LMB seminar bell.

Ever wonder why SGD, which works so well for ab initio cryo-EM, never seems to get to high resolution on its own? Well, we have the answer: conditioning!

Standards for MicroED pubmed.ncbi.nlm.nih.gov/40539937/ #cryoEM

Alves, Andrews, McBean, Wells, El-Gomati, Burkhalter, Schulze-Briese, Zambon, McMullan, Henderson, Russo, Jones: The Dublin Lens: A Cc=1.0 mm Objective Lens Intended for CryoEM at 100 keV https://arxiv.org/abs/2505.11458 https://arxiv.org/pdf/2505.11458 https://arxiv.org/html/2505.11458

A) Diagram showing how EtfD transfers electrons from beta oxidation to the menaquinol pool in the membrane, linking beta oxidation to oxidative phosphorylation in mycobacteria. B) A growth curve showing the Mycobacterium smegmatis lacking EtfD can grow when glucose is provided as the carbon source, but has a slight growth delay. Complementing the ∆etfD strain with M. tuberculosis on a plasmid rescues the defect. C) A growth curve showing that ∆etfD M. smegmatis cannot grow on medium where the fatty acid oleic acid is the only carbon source. A plasmid with with M. tuberculosis EtfD rescues the defect.

EtfD links beta oxidation to OxPhos in mycobacteria - recent work suggests that targeting EtfD could shorten #tubeculosis treatment.
But how does EtfD work? And how can you assay its activity?
In his final PhD manuscript @courbongautier.bsky.social provides answers!
www.biorxiv.org/content/10.1...

1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.

Close to recreating it in ChimeraX:

1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20

Room for improvement, needs more desaturation

Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier The mitochondrial pyruvate carrier transport mechanism is ΔpH driven and is inhibited competitively by distinct compound classes.

Our paper is finally out: Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier | Science Advances www.science.org/doi/10.1126/...
#mitochondria #cryo-EM

RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes

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

Molecular and functional profiling of Gαi as an intracellular pH sensor - Nature Communications Here, the authors identify human Gαi protein as an intracellular pH sensor. The Gαi subunit undergoes a disorder to order transition as pH is increased over the intracellular pH range, which modulates...

Cool!
Molecular and functional profiling of Gαi as an intracellular pH sensor
www.nature.com/articles/s41...

AlphaFold as a Prior: Experimental StructureDetermination Conditioned on a Pretrained Neural Network https://www.biorxiv.org/content/10.1101/2025.02.18.638828v1

Research Group Leader Tenure Track - Structural Studies - LMB 2549 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12835196 Research Group Leader Tenure Track Starting Salary £65,940 to £74,448 per annum MRC Laboratory of Molecular Biology, Cambridge, UK

We have an exciting opportunity for a new independent group leader with an interest in structural/molecular biology and machine learning to join our Division of Structural Studies at the @mrclmb.bsky.social! 🥳
Re-posts appreciated.

www.nature.com/naturecareer...

Protein structure embeddings reveal undersampled and de novo structure space. (B) First two principal components of mean-pooled ESM3 embeddings colored by helix content determined by DSSP. The indicated dashed guide lines denote visual boundaries of native structure space not sampled (Undersampled) and novel regions of protein structure for this space only observed in samples but not in native structures (De novo). (C) Rasterized visualization of panel B with 16 equally spaced grid squares in each principal component axis. A representative structure from each grid was chosen at random. Empty grid squares indicate the absence of any structure in the enclosed region. De novo alpha helices are shaded along the lower-right diagonal and the structures from CATH which do not have corresponding structures in the samples are shaded along the left and top rims. The structures are displayed in CATH raster plot are given in the Supplementary Information.

Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...

We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!

Off-axis electron holography of unstained bacteriophages: Toward electrostatic potential measurement of biological samples pubmed.ncbi.nlm.nih.gov/39818354/

iAPEX: Improved APEX-based proximity labeling for subcellular proteomics using an enzymatic reaction cascade Ascorbate peroxidase (APEX) is a versatile labeling enzyme used for live-cell proteomics at high spatial and temporal resolution. However, toxicity of its substrate hydrogen peroxide and background la...

Proud to share our work spear-headed by PhD student Tommy Sroka with major contributions by #xenopus expert Kerstin Feistel.

Our iAPEX #ProximityLabeling method for #MassSpec based subcellular #proteomics works by locally generating H2O2 using a D-amino acid oxidase that activates APEX2 in situ.

In a great collaboration with @hummerlab.bsky.social and the Kräusslich lab: HIV capsid doesn't break at the NPC; instead, it cracks open the NPC itself! Details in Cell: authors.elsevier.com/sd/article/S... @mpibp.bsky.social @uniheidelberg.bsky.social A thread below:

Opening slide for state of the lab PowerPoint presentation.

Gave our first state of the lab address this week. I broke down the cost of science, from people to stuff. Dove into spending compared to budgets. Spent time on grant submissions and manuscript/project expectations for the year.

I want to be as transparent as possible & this was a great start! 🧪🧠👩‍🔬

Scientific Director, Cal-Cryo@QB3, UC Berkeley’s Cryo-EM Facility University of California, Berkeley is hiring. Apply now!

Scientific Director, Cal-Cryo. We are looking for an outstanding microscopist to run our cryo-EM facility (two Krioses and an Arctica), increase training, engagement, and collaboration on campus, expand our user base, and join our community of cutting edge cryo-EM researchers. tinyurl.com/ykasna3p

If international people are keen to come to the UK then York would love to host them for a Newton Fellowship:
royalsociety.org/grants/newto...

We have brilliant centres for structural biology, chemical biology, parasitology, haematology, atmospheric science, and much more

New development in #cryoEM specimen preparation from the Efremov lab that enables structure determination from a single plate of cells. Will be exciting to see how this revolutionizes low copy structure determination and investigations from native sources.

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

Full disclosure, at risk of revealing the full extent of my ineptitude, the last time I performed motion correction in RELION with a combination of LZW-TIFF/.gain, I merely renamed the gain reference to .tiff. It....didn't seem to mess things up.

I have been similarly confused by this previously. However, I believe the intention behind the phrasing in this section is to say that: relion_convert_to_tiff will output the reciprocal *if* it is necessary--based on the logic in loadEERGain: github.com/3dem/relion/...