John L. Rubinstein

John L. Rubinstein


BSc, University of Guelph, 1998
PhD, Cambridge University, 2002

Address Rm. 20-9705
Peter Gilgan Centre for Research and Learning
The Hospital for Sick Children
686 Bay Street, Toronto
Toronto, ON M5G0A4
Lab The Rubinstein Laboratory
Office Phone 416-813-7255

John Rubinstein obtained his B.Sc from the University of Guelph in 1998. He received his PhD from Cambridge University (2002) where he worked in Medical Research Council laboratories under the supervision of Sir John E. Walker and Dr. Richard Henderson. Dr. Rubinstein was a Postdoctoral Research Associate at the MRC Laboratory of Molecular Biology before returning to Canada for a National Cancer Institute of Canada (NCIC) postdoctoral fellowship at the Banting and Best Department of Medical Research. He joined the Research Institute of The Hospital for Sick Children in 2006 and is a Professor in the Departments of Biochemistry and Medical Biophysics.

Research Lab

F20 microscope at the Rubinstein Lab

Our group, consisting of biophysicists and biochemists, studies the structure and function of macromolecular assemblies using electron cryomicroscopy (cryo-EM), image analysis, biochemistry and molecular genetics.

Current lab members:

  • Yazan Abbas, PhD (Postdoctoral fellow)
  • Stephanie Bueler, MSc (Research Project Coordinator)
  • Samir Benlekbir, PhD (Microscopy facility manager)
  • Yingke Liang (Graduate student)
  • Justin Di Trani, PhD (Postdoctoral fellow)
  • Hui Guo (Graduate student)
  • Yong Zi Tan, PhD (Postdoctoral fellow)
  • Thamiya Vasanthakumar (Graduate student)
  • Hanlin Wang (Graduate student)
  • David Yanofsky (Graduate student)

Learn more: The Rubinstein Laboratory

Research Description

Electron Cryomicroscopy of Macromolecular Machines

Our group studies the structure and function of macromolecular assemblies using electron cryomicroscopy (cryo-EM), image analysis, molecular biology and molecular genetics. We also develop the tools of cryo-EM so that we can answer questions that are not amenable to the techniques that currently exist. This process usually occurs at the level of developing new algorithms and software for image analysis and performing calculations with images and models of molecular structure.

Recent biological projects have included the structural study of the mitochondrial ATP synthase, the Vacuolar-type ATPase, and the V/A-ATPase. We also study bacterial toxins that interact with mammalian cells.

Gatan K2 Summit direct electron detector

Gatan K2 Summit direct electron detector

Tools of Cryo-EM Website

The primary purpose of this dedicated webpage is to disseminate original software for computational analysis of cryo-EM images.  This software is provided as source code and is without any guarantee of support.

Awards & Distinctions

2021 — National Lecturer, Biophysical Society of Canada
2020 — Doctorate of Philosophy honoris causa, Stockholm University
2014-2021 — Canada Research Chair in Electron Cryomicroscopy (Tier I)
2014 — GE Healthcare New Investigator Award (Canadian Society for Molecular Biosciences)
2013 — Burton Medal (Microscopy Society of America)
2009-2014 — Early Researcher Award
2007-2012 — CIHR New Investigator Award

Courses Taught

BCH 2138H Advanced Electron Microscopy
BCH 2024H Intro to X-ray crystallography and electron cryomicroscopy
BCH473Y Advanced Research Project in Biochemistry
BCH425H Structural Biology: Principles and Practice


View all publications on PubMed

Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline
Hui Guo, Gautier M. Courbon, Stephanie A. Bueler, Juntao Mai, Jun Liu, and John L. Rubinstein
(2021) Nature 589, 143-147

Through-grid wicking enables high-speed cryoEM specimen preparation
Yong Zi Tan and John L. Rubinstein
(2020) Acta Cryst D76, 1092-1103.

Structure of V-ATPase from the mammalian brain
Yazan M. Abbas, Di Wu, Stephanie A. Bueler, Carol V. Robinson, and John L. Rubinstein
(2020) Science 367, 1240-1246.

Structural comparison of the vacuolar and Golgi V- ATPases from Saccharomyces cerevisiae
Thamiya Vasanthakumar, Stephanie A. Bueler, Di Wu, Victoria Beilsten-Edmands, Carol V. Robinson, and John L. Rubinstein
(2019) PNAS 116, 7272–7277

Atomic model for the dimeric FO region of mitochondrial ATP synthase.
Hui Guo, Stephanie A Bueler, and John L Rubinstein
(2017) Science 358, 936-40.

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, and Marcus A Brubaker
(2017) Nature Methods 14, 290-6

Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.
Mohammad Mazhab-Jafari, Alexis Rohou, Carla Schmidt, Stephanie A Bueler, Samir Benlekbir, Carol V Robinson, and John L Rubinstein
(2016) Nature 539, 118-22.

Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase
Jianhua Zhao, Samir Benlekbir, and John L. Rubinstein
(2015) Nature 521, 241-5.

Alignment of cryo-EM movies of individual particles by optimization of image translations
John L. Rubinstein and Marcus A. Brubaker
(2015) Journal of Structural Biology 192, 188-95.