John Rubinstein @johnrubinstein.bsky.social · 30/09/2026A new PhD is formed. Congratulations @zestytoast.bsky.social on a spectacular defense! And thanks to Christina Stallings for serving as external examiner (and guest speaker) 1131
John Rubinstein @johnrubinstein.bsky.social · 24/09/2026The @structurabio.bsky.social @sickkidsto.bsky.social CryoSPARC workshop is underway! 041
John Rubinstein @johnrubinstein.bsky.social · 06/07/2026CryoSPARC workshop in Toronto! Beyond consensus refinements: Advanced cryo-EM data processing with CryoSPARC Sept 24-25, 2026 (part of the Canadian Cryo-EM Nexus) Register here: cvent.me/dL1wem Please see details in the link or the image Alt text @structurabio.bsky.social @sickkidsto.bsky.social 12513
John Rubinstein @johnrubinstein.bsky.social · 04/07/2026New preprint! Karin Schumacher's postdoc Nadja used our SidK approach to purify Arabidopsis V-ATPase & Mariia Khamina determined its structure. The structure shows unique plant V-ATPase features and that TLDc proteins (here OXR5) bind V-ATPase in all eukaryotes. 🌱 tinyurl.com/mw9xaszk 0285
John Rubinstein @johnrubinstein.bsky.social · 16/05/2026Overdue post (busy week): After seeing @zestytoast.bsky.social's structure of mycobacterial NDH-2, Ruben & Baptiste (@inserm.fr) asked if we could get a structure with one of their remarkable tricyclic-spirolactams Their study & Yingke's structure now out in ChemRxiv! chemrxiv.org/doi/full/10.... 0132
John Rubinstein @johnrubinstein.bsky.social · 01/05/2026After two days in the beautiful new SickKids Patient Support Centre, the first @sickkidsto.bsky.social @structurabio.bsky.social CryoSPARC workshop is now in the books! Outstanding teaching by Rich Waldo from Structura, and logistics by Samir Benlekbir (SickKids) and Saara Virani (Structura). 0192
John Rubinstein @johnrubinstein.bsky.social · 22/04/2026I love it when I walk into the lab and it looks like a staged photo for collaborative science. 0150
John Rubinstein @johnrubinstein.bsky.social · 19/04/2026Was just asked to spread the word about this position. Structural biology and Chemical Biology positions in Barcelona, one of the great cities of the world! www.irbbarcelona.org/sites/defaul... 01620
John Rubinstein @johnrubinstein.bsky.social · 04/04/2026Sad news on the passing of Prof. Andreas Engel, a pioneer in the field of cryo-EM (shared with the 3DEM community by Henning Stahlberg). Andreas' kindness, warmth, and enthusiasm for science and his colleagues will be missed. 05726
John Rubinstein @johnrubinstein.bsky.social · 03/04/2026It was @courbongautier.bsky.social 's last day in the lab. He came to the lab, did some amazing science, had some fun, and leaves an accomplished scientist. And he leaves this place, and all of us here, changed for the better. 0160
John Rubinstein @johnrubinstein.bsky.social · 28/03/2026Congratulations on a great PhD defense @ianyyen.bsky.social! I've enjoyed discussing the finer points of cryo-EM with Ian, being on his advisory committee, and having him as an "honorary group member" these past 6 years. 1173
John Rubinstein @johnrubinstein.bsky.social · 17/03/2026When it rains myco publications in pours myco publications! Now out in PNAS tinyurl.com/2a6833n4 When @zestytoast.bsky.social accidentally isolated the long-chain acyl-CoA carboxylase, we quickly realized we were looking at a fascinating machine essential for building the mycobacterial membrane... 24717
John Rubinstein @johnrubinstein.bsky.social · 17/03/2026Out now in EMBO J ahead of World #TB day! Our friends at the TB Drug Accelerator identified EtfD as a high-priority target for fast acting treatments so @courbongautier.bsky.social jumped into action. Our EtfD assay & struct are already being used to help find new therapeutics tinyurl.com/3cb2j5k9 0338
John Rubinstein @johnrubinstein.bsky.social · 06/03/2026I've written a review on what I think is an extremely exciting direction in cryo-EM: Cryo-EM of endogenous membrane proteins in their native lipid bilayer Open access in Quarterly Reviews of Biophysics: doi.org/10.1017/S003... 317765
John Rubinstein @johnrubinstein.bsky.social · 13/02/2026Deadline approaching to register for the @structurabio.bsky.social & @sickkidsto.bsky.social CryoSPARC workshop in Toronto! Open to all, this is a unique opportunity to learn CryoSPARC from the experts at Structura. April 30/May, 2026. For more information and to register: tinyurl.com/y42pf4wy 099
John Rubinstein @johnrubinstein.bsky.social · 05/02/2026A new frontier for our lab! After many months of development by postdoc @ranaabdelaziz.bsky.social (our resident medicinal chemistry - now also an excellent structural biologist) and the staff at the SickKids Drug Discovery platform, we're conducting our first proof-of-principle inhibitor screen. 5443
John Rubinstein @johnrubinstein.bsky.social · 31/01/2026I don't think numerical resolution is the right thing to think about here. If I want to say this Lys points 'up', the map density supports the claim that it extends in that direction. (Random map/model I had open in ChimeraX, nominally 3.2 Å res'n but I don't know the local res'n) 020
John Rubinstein @johnrubinstein.bsky.social · 30/01/2026@structurabio.bsky.social and @sickkidsto.bsky.social CryoSPARC workshop in Toronto! April 30/May 1st 2026. Part of the Canadian Cryo-EM Nexus. Please register here: sickkids.cventevents.com/event/a0aebb... 0116
John Rubinstein @johnrubinstein.bsky.social · 09/01/2026Congratulations to the new Doctor of Philosophy @courbongautier.bsky.social on a spectacular PhD defense following a groundbreaking PhD! Thanks to external examiner Damian Ekiert from JHU and the rest of the examining committee. Next stop, Oxford University for a postdoctoral fellowship. 🇫🇷🇨🇦🇬🇧 2363242
John Rubinstein @johnrubinstein.bsky.social · 06/01/2026Some of the earliest photos from the lab... 050
John Rubinstein @johnrubinstein.bsky.social · 06/01/2026In Jan 2006 I started my dream job: running my own research group at The Hospital for Sick Children in my home town, Toronto. Stephanie Bueler started as lab manager on Day 1. Many students, postdocs, papers, and microscopes later we're still going strong - and Stephanie is still putting up with me! 1515
John Rubinstein @johnrubinstein.bsky.social · 16/12/2025I never get tired of this view from the lab 11114
John Rubinstein @johnrubinstein.bsky.social · 12/12/2025The lab's entry into the annual Cell Biology + Molecular Medicine gingerbread house competition (no contribution from me). The faux Greek writing pains me, but the construction is brilliant! 2170
John Rubinstein @johnrubinstein.bsky.social · 30/10/2025Oops, the picture of mycolic acids (from en.wikipedia.org/wiki/Mycolic...) in the previous skeet isn't displaying properly. Here it is again. 000
John Rubinstein @johnrubinstein.bsky.social · 30/10/2025Thanks! Yes, lots of great work has been done on related complexes! The mycobacterial LCC is pretty weird compared to the others, though: it has one type of subunit (AccD5) for acetyl/propionyl-CoA and another (AccD4) for very long chain acyl-CoA, used to form the alpha branch of mycolic acid: 110
John Rubinstein @johnrubinstein.bsky.social · 30/10/2025Interestingly, Yingke found some complexes bound to uncharacterized proteins MSMEG_0435 & 0436 (Rv0263c & 0264c in M. tuberculosis). A recent preprint from Carl Nathan shows that Rv0263c is needed for Mtb survival during transmission, suggesting it modulates mycolic acid synthesis in TB transmission 141
John Rubinstein @johnrubinstein.bsky.social · 30/10/2025A structure with short- and long-chain acyl-CoAs shows how the two types of carboxyltransferase (CT) subunit distinguish acyl-CoAs: the short-chain CT subunit binds CoA but can’t accommodate a long acyl chain; the long-chain CT subunit binds long acyl chains but doesn’t interact strongly with CoA. 120
John Rubinstein @johnrubinstein.bsky.social · 30/10/2025Adding short-chain acyl-CoA substrate (plus ATP & bicarbonate) causes biotin carboxyl carrier protein (BCCP) domains to travel between biotin carboxylase (BC) domains, which load a carboxyl group onto the BCCP biotin, and the carboxyltransferase (CT) domain, which transfers it to the acyl-CoA. 120
John Rubinstein @johnrubinstein.bsky.social · 30/10/2025The MCC complex is well studied, but the long-chain carboxylase (LCC) complex isn’t, and is essential for making mycolic acid for the mycobacterial cell wall. The LCC complex carboxylates both long-chain and short-chain acyl-CoA. A structure with propionyl-CoA shows how it binds short-chain acyl-CoA 120
John Rubinstein @johnrubinstein.bsky.social · 30/10/2025New lab preprint! @zestytoast.bsky.social tagged a scarce mycobacterial protein in M. smegmatis with TwinStep but got… something? @kjamali.bsky.social's ModelAngelo built models & @martinsteinegger.bsky.social's FoldSeek IDed them as the biotin-containing MCC & LCC complexes 🧵 tinyurl.com/ukny4ptz 49030
John Rubinstein @johnrubinstein.bsky.social · 15/08/2025Whoever designed the new landscaping around King's College Circle at @utoronto.ca has done a brilliant job! All summer I've been getting off the subway early to walk down Philosopher's Walk and the new walkways on the St. George campus - a great half hour start to each day. 0130
John Rubinstein @johnrubinstein.bsky.social · 12/07/2025Returned 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. 3597
John Rubinstein @johnrubinstein.bsky.social · 24/06/2025Very proud of my amazing wife, Dr. Voula Kanelis, awarded a King Charles III coronation medal yesterday for her contributions to Heart & Stroke Canada (❤️ / ). 0270
John Rubinstein @johnrubinstein.bsky.social · 22/06/2025My brother, Dan Rubinstein's, latest book is out. Can't wait to dive in! 1120
John Rubinstein @johnrubinstein.bsky.social · 07/06/2025Great to hear about this event. Derek was an awesome guy and one-of-a-kind. He made the world a better place. Derek was a pioneer in cryo-EM. I first met him at the EMBO Workshop in 2000 when he was teaching people how to freeze grids. 020
John Rubinstein @johnrubinstein.bsky.social · 31/05/2025Wow. Amazing retirement symposium for the legendary Sergio Grinstein. Staggering expanses of biology revealed. But the heartfelt stories of generosity, support, and careers launched and sustained really got to me. I spent the entire day verklempt Brilliantly organized by @spencerfreeman.bsky.social 1160
John Rubinstein @johnrubinstein.bsky.social · 16/05/2025We developed an EtfD assay! By mixing mycobacterial inverted membrane vesicles (containing the electron transport chain) with purified proteins for fatty acid oxidation and e- transfer, we can detect when EtfD drives the ETC. This assay will allow for detection and development of EtfD inhibitors. 120
John Rubinstein @johnrubinstein.bsky.social · 16/05/2025One of the iron-sulfur clusters (D1) is a linear [3Fe-4S] cluster that has been synthesized chemically and detected spectroscopically but has not been seen before in the structure of a protein under physiological conditions 121
John Rubinstein @johnrubinstein.bsky.social · 16/05/2025The structure of EtfD reveals a wire of iron-sulfur clusters and a b heme that link the electron transfer flavoprotein (ETF) in the cytosol to a menaquinone binding site in the membrane. Two of the iron-sulfur clusters are pretty weird... 111
John Rubinstein @johnrubinstein.bsky.social · 16/05/2025EtfD 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... 14316
John Rubinstein @johnrubinstein.bsky.social · 10/05/2025I love how scientific ideas and techniques spread from mind to mind and place to place. Spotted this week in Cleveland, Ohio: 0110
John Rubinstein @johnrubinstein.bsky.social · 13/03/2025Hey University of Saskatchewan colleagues: I'm looking forward to giving a lecture there on Thur Mar 27th. Membrane protein structural biology, mycobacterial bioenergetics, and TB drug discovery. Come say 'Hi' 080
John Rubinstein @johnrubinstein.bsky.social · 27/02/2025My own institution doesn't do too badly in the Specialized/Pediatric category (no surprise, knowing my clinical colleagues)... 030
John Rubinstein @johnrubinstein.bsky.social · 27/02/2025Newsweek ranks Toronto's University Health Network (UHN) as 3rd best hospital in world and #1 Public hospital in the world. The two hospitals above it are private businesses. Is this the poor healthcare Donald Trump wants to save Canadian's from? www.newsweek.com/rankings/wor... 2150
John Rubinstein @johnrubinstein.bsky.social · 22/02/2025🚨 Amazing Opportunity 🚨 U Alberta is looking for a director for their new #cryoEM facility Support excellent researchers (who are really nice people) using state-of-the-art infrastructure. + reasonable cost of living + near some of most beautiful places in world + 🇨🇦 apps.ualberta.ca/careers/post... 320850
John Rubinstein @johnrubinstein.bsky.social · 21/02/2025After a long and productive career at The Hospital for Sick Children and the University of Toronto, Prof. Charlie Deber has retired. Saw this in his lab space 🥲 0233
John Rubinstein @johnrubinstein.bsky.social · 19/02/2025We propose a revised integrated model of the mycobacterial electron transport chain and central carbon metabolism (Krebs), with the Krebs cycle tethered to the membrane in multiple places, and preferentially directing electrons to the CIII2CIV2 terminal oxidase and not the cyt. bd terminal oxidase. 120