Basil Greber
@bjgreber
Structural biologist. High-resolution imaging of macromolecular assemblies (and landscapes). MRC career development fellow/group leader at the Institute of Cancer Research, London. Views my own.
Monday: Train cancelled because too many trains need repair. Tuesday: Train cancelled because too many trains need repair. Wednesday: Train delayed because another train broke down. Almost 10% cancellations and just barely more than 70% on time is “not great”. Back to more maintenance, I guess.
Our data clarify how TFIIH enters the NER machinery in its full form, with the CAK bound, and, along with prior structural data from several other labs, they contribute to our growing structural understanding of the mechanisms of NER.
This approach, combined with purified holo-TFIIH (including the CAK), the trimeric XPC complex, and XPA, allowed us to visualise three early-stage NER assemblies from a single grid.
We did this using streptavidin affinity grids, onto which we could immobilise NER assemblies bound to biotinylated DNA. This process was long and painful, and we are grateful for the excellent protocols from @trinitycookis.bsky.social et al. from the @nogaleslab.bsky.social that helped us a lot.
It is almost over, so this seems to be a good time to share a few photos taken during the DNA repair meeting in Egmond aan Zee (mostly in the early mornings before sessions). What a fantastic setting to hold a conference!
To round off our story, we have additionally determined structures of OTS964 bound to its target, CDK11, as well as two off-target CDKs. OTS964 is a kinase inhibitor that is currently being developed towards therapeutic application in cancer treatment.
When we inspected our densities, we found something unusual: The substrate binding pocket of CDK11 was blocked... by a part of CDK11 itself. This CDK11 segment looks rather similar to substrate peptides observed in previous structures of other CDKs. What could this protein segment be doing there?
I had previously attempted to purify a CDK11-cyclin L complex and failed miserably. Amy figured out that adding SAP30BP enabled the isolation of a stable complex. It turns out that SAP30BP stabilises the CDK-cyclin interactions by forming molecular contacts with both proteins.
Have a look at our latest results on #CDK regulation, just posted as a pre-print! This study was spearheaded by PhD student Amy McGeoch. Amy has determined the #cryoEM structure of the CDK11-cyclin L-SAP30B complex, an important regulator of #spliceosome activation. www.biorxiv.org/content/10.6...
It's (almost) a wrap. After a bit more than two weeks in highly photogenic Vietnam, it is time to head home and face the world again. #travelphotography #nikon
SLX4 and XPF-ERCC1 participate in the formation of a huge multi-nuclease complex called SMX, which has been studied intensively by many labs. We are happy to contribute the structural details of the SLX4-XPF recruitment interface to the pool of data that helps us understand this molecular puzzle.
It turned out that these segments participate in stimulating the enzymatic activity of XPF-ERCC1. Please note that this figure is rendered oddly in the uncorrected proof - the image below is how it will look in the final version of the paper.
Structure determination of a DNA-bound XPF-ERCC1-SLX4-SLX4IP complex allowed us to identify segments of SLX4 that are visualised only in the DNA-bound state of the complex.
We started out with AlphaFold predictions and #cryoEM structures that show the interactions between the endonuclease XPF-ERCC1, the scaffold protein SLX4, and the DNA repair factor SLX4IP. This allowed us to pinpoint and test the molecular interactions that govern complex assembly.
Our latest paper on the molecular mechanisms of XPF-ERCC1 recruitment to SLX4-dependent DNA repair pathways has been published! Congratulations to first author Junjie Feng, and a heartfelt thank you to all our collaborators for their contributions to this study! www.nature.com/articles/s41...
To further support this idea, we determined structures of CAK-CDK1-cyclin B and CAK-CDK11. Which agreed with the predictions and our hypothesis. This suggests that we have uncovered a general mechanism for CDK activation by the CDK-activating kinase.
Does this arrangement also apply to other CDKs that are activated by the CAK? We ran AlphaFold3 predictions, which suggested that this architecture was indeed shared across multiple CAK-CDK complexes.
We started out on this journey by determining structures of CAK-CDK2 and CAK-CDK2-cyclin A complexes. They revealed a pseudo-symmetric arrangement of CDK7 and its substrate, CDK2. Biochemical analysis demonstrated that contacts in both kinase lobes are important for this interaction.
I guess I am late to the party, but the new Rainbow Rocket bouldering gym in Cambridge is pretty cool!
Couple snaps from our recent family trip to the (very pretty) seaside in Dorset. #landscape #landscapephotography #nikon
And last but not least, some from team displays - the Frecce Tricolori and the Royal Jordanian Falcons - accompanied by a close-up of an F/A-18 front section.
A few more - including the Danish F-16, a few Spitfires, a Hurricane, and a Lancaster.
A few photos from this year's @airtattoo.bsky.social (which took place 10 days ago not too far from home). The weather was highly variable, but it made for interesting backgrounds in the photos. Descriptions in alt text. #aviation #airshow #aviationphotography