John Rubinstein

@johnrubinstein.bsky.social

2288 Followers 554 Following

CryoEM, Bioenergetics, V-ATPases (especially in synaptic vesicles and lysosomes), OxPhos (especially in mycobacteria as a TB drug target) Scientist, The Hospital for Sick Children Professor, U of Toronto 👨‍👩‍👧🔬🚲 rubinsteinlab.org COI: structura.bio

Workshop announcement graphic shows a classroom scene with the CryoSPARC logo and workshop title, date, and hosting organizations (SickKids and Structura Biotechnology) Workshop information: As part of the Canadian Cryo-EM Nexus, The Hospital for Sick Children (SickKids) and Structura Biotechnology are pleased to announce a two-day CryoSPARC workshop: Beyond consensus refinements: Advanced cryo-EM data processing with CryoSPARC at SickKids in Toronto on September 24-25, 2026. Led by experts from Structura, this workshop offers a unique opportunity for participants who already have a sound understanding of cryo-EM and substantial CryoSPARC experience to deepen their skills and become a key resource for cryo-EM image analysis within their institutions. There is $115 (CAD) charge to partially defray some of the costs of running the workshop, which is sponsored by SickKids and Structura. Attendees will need to bring their own laptop computer and arrange for travel and accommodation. Please apply before July 24, 2026 using the following link: https://cvent.me/dL1wem
Overall structure of Arabidopsis V-ATPase. (A) SDS-PAGE of purified V-ATPase. (B) Composite map of Arabidopsis V-ATPase in rotational state 1. (C) Atomic model of Arabidopsis V-ATPase in rotational state 1. (D) Cross sections of the V1 and VO regions in three rotational states. (E) Conformations of subunit H in V-ATPase structures of Arabidopsis V-ATPase (top) and the citrus fruit (bottom) V-ATPase.
Table showing chemical structures of several of the tricyclic spirolactams synthesized in the study, including BDM91465
A classroom of cryo-EM scientists, their brains recently filled with the latest and greatest methods for cryo-EM image analysis.
Photo of a laboratory bay full of computers. Three scientists stand around one computer on one side of the bay, while two scientists examine another computer on the other side.
IRB Barcelona invites applications for Group Leader positions in Chemical Biology (one) and Structural Biology (one) as part of its strategic effort to strengthen molecular sciences. The successful candidates will join a highly multidisciplinary and collaborative institute with strong expertise in cancer and metastasis, ageing and cell reprogramming, metabolism, cell differentiation, signal transduction, and gene expression, working at the interface of structural and computational biology, chemistry, and biology. IRB Barcelona is embedded in a vibrant scientific ecosystem and maintains close collaborations with major research infrastructures such as the Barcelona Supercomputing Center (BSC) and the ALBA Synchrotron, as well as leading research centres, universities, and hospitals in Barcelona. About IRB Barcelona IRB Barcelona (www.irbbarcelona.org) is a multidisciplinary research institute where scientists collaborate to address fundamental biomedical questions and unmet medical needs. The Institute currently hosts more than 500 members from around the world across 27 research groups. How to apply Applications should include a CV, letter of intent, brief (2-page) research proposal, and the names and contact details of at least three referees. Applications must be submitted via https://recruitment.irbbarcelona.org no later than 22 May 2026, quoting reference GL/26/01 (Chemical Biology) or GL/26/02 (Structural Biology). The successful candidates are expected to join in Q4 2026 or 2027, with flexibility depending on individual circumstances. For Informal enquiries, please contact the chair of the Search Committee (Prof. Xavier Salvatella, at xavier.salvatella@irbbarcelona.org) and for details and updates on the selection process please contact the Head of People at (irbglcall@irbbarcelona.org)
Dear colleagues, With deep sadness I share the news that Andreas Engel passed away last Wednesday, at the age of 82, after a courageous fight against an aggressive caner. Only half a year ago, he was out hiking in the Italian mountains with his wife Barbara, walking 160 km in a single week. Andreas trained as a physicist in Bern, Switzerland, before heading to John Hopkins University in Baltimore for his postdoctoral work. He then led a research group at the Biozentrum in Basel, and in 1985 took on the role of a group leader in research and development at Ilford Ltd. in Fribourg, Switzerland. In 1987, he joined forces with his colleague Ueli Aebi to establish the Maurice E. Müller Institute at the Biozentrum of the University of Basel. Together, Ueli and Andreas served as professors for structural biology there for almost a quarter century, leaving a lasting mark on the field of structural biology as we know it today. Andreas Engel was a true pioneer. He was among the first to apply atomic force microscopy (AFM) with the tip operating under water, and one of the earliest researchers to perform 3D reconstructions using scanning transmission electron microscopy, achieving remarkable high-resolution maps of porin 2D crystals by STEM. He became a leading expert in membrane protein 2D crystallization, and his group played a key role in the determination of the first aquaporin structure, in collaboration with Peter Agre and Yoshinori Fujiyoshi. As he approached retirement from Basel, Andreas founded the Center for Cellular Imaging and NanoAnalytics (C-CINA) of the University of Basel, which in 2009 operated among others one of the very early Titan Krios instruments. From 2008 also held a professorship at Case Western Reserve University, Cleveland, followed by a position at TU Delft in the Netherlands in 2013. In 2020, he was among the founding members of CryoWrite, a company in Basel that he led as CEO until recently. His contributions to science, to the tools of str…
John and Gautier pose for a photo
Bob at the Grand Hotel in Stockholm ahead of the Nobel Prize ceremony in 2017
A group photo of Ian with some of his friends from the 20th Floor Molecular Medicine. Everyone but Ian is wearing a tee shirts with a picture of Ian on it.
On the left a light blue density map shows the structure of EtfD in a model membrane in orange. On the right, a schematic shows the path of electrons from beta-oxidation going ETF (the electron transfer flavoprotein) through four iron-sulfur clusters and a heme to reduce menaquinone in the EtfD structure.
Figure 1. Cryo-EM of abundant protein complexes in native membranes.
The Structura logo with dates for the workshop listed. The bottom reads "Hosted by SickKids and Structura Biotechnology"
A robotic system moves 384 well plates between and ultrasonic liquid dispensing device and a plate reader.
Dear Colleagues, As part of the Canadian Cryo-EM Nexus, The Hospital for Sick Children (SickKids) and Structura Biotechnology are hosting a two-day CryoSPARC workshop at SickKids in Toronto on April 30 and May 1, 2026. Led by experts from Structura, this workshop offers a unique opportunity for participants with prior CryoSPARC experience to deepen their skills and become a key resource for cryo-EM image analysis within their institutions. Applicants should have hands-on experience with CryoSPARC, demonstrated by having processed at least two datasets, and must be committed to sharing their expertise with colleagues upon returning to their home institution. There is no charge for participating in the workshop, which is sponsored by SickKids and Structura. Attendees will need to bring their own laptop computer and arrange for travel, accommodation, and meals. Given the limited capacity (15 students), we kindly request that interested individuals ensure that they can cover these costs before registering. Please register before February 20, 2026 using the following link: https://sickkids.cventevents.com/event/a0aebb07-66e6-4cbe-b471-8009fe0c227c/summary?i=97c975e9-4bac-42b9-a1b2-95974110db9e&tm=DXVv8zGvH5uA7nqj8lEF4iifi-ukLal5QBBjdXWGD2E&locale=en-US We look forward to welcoming you to this workshop. Sincerely, Samir Benlekbir and John Rubinstein (SickKids) & CryoSPARC Team (Structura)
Gautier Courbon stands at a podium presenting the acknowledgements slide from his PhD defense talk.
John (left) tries to get his lab to place the field emission gun on top of the column of the lab's new Tecnai F20 microscope (circa 2007). PhD student Wilson Lau (now Associate Prof, Hong Kong Polytechnic University), lab manager Stephanie Bueler (still managing the lab), and PhD student Lindsay Baker (now Associate Prof, Oxford University) make a valiant effort.
A young John Rubinstein and Stephanie Bueler on a lab skating trip at Nathan Philip Square in Toronto..
Dusk view of Toronto south toward Lake Ontario from The Hospital for Sick Children's PGCRL research tower (20th floor)
A gingerbread house that looks like the Parthenon, with a sign in faux Greek writing that reads "Parthe nom nom nom". A sign on the side reads "Rubinstein Labz 2025 BC"
Chemical structures of mycolic acid (from wikipedia) showing different modifications of the myromycolate chain.
Cryo-EM map (left) and atomic model (middle and right) showing that the uncharacterized proteins MSMEG_0435 and 0436 bind the LCC complex. These proteins were identified with ModelAngelo and FoldSeek and also detected by mass spectrometry of the sample.
Movie showing the LCC complex and the multiple positions of the biotin carboxyl carrier protein (BCCP) domain when the sample is frozen with short-chain acyl-CoA, ATP, and bicarbonate.
Assay showing that the LCC complex has propionyl-CoA carboxylase activity (left). A cryo-EM map with propionyl-CoA (middle and right) shows where the short-chain acyl-CoA binds in the AccD5 subunit.
Cryo-EM maps and atomic models of the biotin-containing 3-methylcrotonyl-CoA carboxylase (MCC) complex and long-chain acyl-CoA carboxylase (LCC) complex
U of T's Philosopher's Walk, with the Royal Ontario Museum on the left and the Royal Conservatory of Music's Koerner Hall on the right.
At Darwin College: Richard Henderson Jacqueline Milne Sriram Subramanian Nigel Unwin David Barford Da-neng Wang John Rubinstein
Voula Kanelis
Cover of Water Borne, a 1,200-mile paddleboarding pilgrimage, by Dan Rubinstein. Cover photo shows a Dan on his paddleboard on open water, with dry bags tied at the bow and stern. Available at all good bookstores now!
Derek Mills and John Rubinstein. Switzerland, 2017
Post symposium comments by an overwhelmed Sergio, with an equally drained Spencer Freeman standing by his side.
A) Schematic of the EtfD (+FadE5 and ETF) activity assay. The substrate butyryl-CoA is oxidized by FadE5, which transfers electrons to ETF, which then transfers electrons to EtfD. EtfD reduces menaquinone in the membranes of inverted membrane vesicles (IMVs) to menaquinol, which drives ETC activity. This ETC activity is detected by fluorescence quenching of the fluorophore ACMA, while nigericin allows subsequent fluorescence recovery. B) Butyryl-Co-A does not drive proton pumping in wildtype IMVs until purified ETF (which is contaminated with or a bit of FadE5) or FadE5 (which is contaminated with a bit of ETF) is added. Adding both ETF and FadE5 leads to robust proton pumping. C) IMVs from ∆etfD do not exhibit butyryl-CoA-driven proton, but rescue of ∆etfD with a plasmid encoding M. tuberculosis EtfD restores this activity D) Control experiment showing that all of the IMVs are capable of succinate-driven proton pumping, as expected.
Movie showing the experimental density in the cryo-EM map for the four iron-sulfur clusters
A) Cryo-EM map and atomic model for EtfD B) Schematic of domain architecture of EtfD C) Cartoon showing the wire of four iron-sulfur clusters (D1-D4) and heme b linking the input of electrons from ETF to the menaquinone-reducing site in the membrane D) Experimental density for D1-D4, heme b, and the menaquinone site D1 is linear [3Fe-4S] cluster that has been synthesized and detected spectroscopically not been seen before in the structure of a protein under physiological conditions (!!!). D2 is a non-cubane [4Fe-4S] cluster D3 and D4 are cubane [4Fe-4S] clusters
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.
A great white trillium flower
An old-school, custom-made, cryo-EM grid freezing device.
University of Saskatchewan logo
Public domain photo of Banff national park in Alberta, Canada.
Whiteboard cartoon of Dr. Charlie Deber with the message "Thank you for everything !". Artist unknown.
Email announcing that the current Vanier Canada Graduate Scholarship competition and Banting Postdoctoral Fellowship competition will be the last.
Schematic depiction of the mycobacterial oxidative phosphorylation system, including the electron transport chain (Complex I,NDH-2, two succinate dehydrogenases, the CIII2CIV2 respiratory supercomplex Cyt. bcc-aa3, and Cyt. bd) and the ATP synthase.
Redacted email from a parent thanking John for mentoring their daughter.
Overall structure of mycobacterial NDH-2 (class II NADH dehydrogenase) dimer. NDH-2 is the primary entry point for electrons into the mycobacterial electron transport chain. Electrons are transferred from NADH to menaquinone via an FAD cofactor.
Closeup image of a bowl with part of the Congee Queen logo visible
Frost pattern on an old window
A gingerbread house that resembles the Notre-Dame de Paris cathedral, with baguette columns.
Two responses to a message that share the same format but different content.
Three persimmons: two nonastringent Fuyu persimmons on the left and one astringent Hachiya persimmon on the right.