We made the cover! Presenting the #photosystem of Gemmatimonas phototrophica, a funky little bacterial alga (the first discovered example of its genus) found in the Gobi desert a little under a decade ago. This one's been quite the journey, so buckle in. (1/) What I'd mostly like to talk about is the saga of how this model came to be... but first, a little about what makes it special. At first glance, it's fairly similar to other bacterial photosystems: a central reaction complex (RC) surrounded by a light-harvesting (LH) ring. (2/)

For your delectation: the Rhodobacter sphaeroides LH2 antenna complex at a glorious 2.1 Angstrom resolution. Building this one was an absolute joy, with maps (courtesy of new-to-Twitter @PuQian3) so good they almost felt like cheating! (1/7)

https://twitter.com/DavSwain/status/1453095353381707779

Remember the big RC-LH1 dimer complex from a few weeks back? These smaller LH2 complexes act as little satellites to that, increasing the light-gathering area and passing their excitation energy back to the LH1 complex. (2/7)

https://twitter.com/CrollTristan/status/1446857820175994889?s=20

There's (quite rightly) a lot of raving about the new AlphaFold DB resource today. Thought I'd weigh in with my own example. DNA-dependent protein kinase catalytic subunit (uniprot.org/uniprot/P78527) is an enormous beast - a single chain of 4,128 residues! (1/10)

https://twitter.com/PDBeurope/status/1418511467989684224

There are now 19 structures of this guy in the wwPDB, all post-resolution-revolution cryoEM structures. The first (2017) was reconstructed to a character-building 4.3 Å. I'm told the model building was extremely challenging, ... (2/10)

As we all know by now, the most pressing current concern about the ongoing pandemic is the potential for emergence of immune-escape variants. With that in mind, I'm very happy to have had the chance to contribute to this important work: (1/6)
nature.com/articles/s4158… A major multi-centre effort including @tylernstarr, @jbloom_lab, @Vir_Biotech, @jchodera, @ivyzhang__, @W_Glass and many others, this work assesses a wide panel of antibodies against the SARS-CoV-2 spike for potency, breadth and potential for immune escape. (2/6)

A more extreme illustration of the problem: yes, this is a single residue (JSG, found in 6s8h and 6mhu). What it actually *is* is E. coli lipopolysaccharide (LPS) - how it appears in the database is {deep breath}:

https://twitter.com/CrollTristan/status/1357659731691773953

(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-[(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-5-[(2~{s},3~{s},4~{r},5~{r},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{r},5~{s},6~{r})-6-[(1~{s})-2-[(2~{s},3~{s},4~{s},5~{s},6~{r})-...

As is becoming increasingly common these days, the pace of reality has well outstripped that of the scientific publication cycle. Still, I'd like to share this with you: sciencedirect.com/science/articl… (1/14) Unless you've been entirely disconnected for the last month or three, the core message (that immunity-escaping variants of SARS-CoV-2 are developing and need to be watched) should come as no surprise. This work focuses on one of the first such mutants identified, N439K. (2/14)

ISOLDE 1.0 is finally live! To get it, just install ChimeraX 1.0 from rbvi.ucsf.edu/chimerax/downl…, then go to Tools/More Tools..., find ISOLDE and click Install. In the thread, I'll give a quick recap of what ISOLDE is, followed by a rundown of what's new. (1/17) So what is ISOLDE? In brief, it's an interactive environment for (re)building atomic models into medium-low-density crystallographic and cryo-EM maps using GPU-accelerated interactive molecular dynamics. That's a bit of a mouthful, so here's a video demo in the next tweet. (2/17)

In all cryo-EM maps of the SARS-CoV-2 spike protein density for the N-terminal domain has been really rubbishy, with modelling only really possible based on somewhat-weak homology to the original SARS equivalent... until now. (1/12) On the left: a better-resolved region from this domain in 6vxx - general path of the backbone is fine, but sidechains are uninterpretable without outside info. The outer surface loops devolve to complete rubbish. On the right, the same site from 6zge. Clear, unambiguous (2/12)

I was going to wait until Monday to organise and release my current set of SARS-CoV-2 structure rebuilds, but given that I woke up with a bit of a cough (don't worry, nothing serious yet) I figured better safe than sorry. Link in next post, and previous tweets collated in thread: Link to models: drive.google.com/drive/folders/…. Each folder also contains a short set of notes covering what I considered the most important changes/issues. I'll add the previous threads discussing each model below, and add new ones as I do them.