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:

  • Stephanie Bueler, MSc (Research Project Coordinator)
  • Samir Benlekbir, PhD (Microscopy specialist)
  • Hui Guo, PhD (Postdoctoral fellow)
  • Mohammad Mazhab Jafari, PhD (Postdoctoral fellow)
  • Zev Ripstein, (Graduate student)
  • Daniel Schep (Graduate student)
  • Thamiya Vasanthakumar (Graduate student)
  • Jianhua Zhao (Graduate student)
  • Anna Zhou (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 (a collaboration with the group of Sir John Walker, at the MRC Mitochondrial Biology Unit in Cambridge, UK), 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

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

BCH473Y Advanced Research Project in Biochemistry
BCH425H (JBB1425) Structural Biology: Principles and Practice


View all publications on PubMed

Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.
Anna Zhou, Alexis Rohou, Daniel G. Schep,John V. Bason, Martin G. Montgomery, John E. Walker, Niko Grigorieff, and John L. Rubinstein
(2015) eLife e10180.

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

Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images
Jianhua Zhao, Marcus A. Brubaker, Samir Benlekbir, and John L. Rubinstein
(2015) ArXiv 1501.05928

Alignment of cryo-EM movies of individual particles by optimization of image translations
John L. Rubinstein and Marcus A. Brubaker
(2014) ArXiv 1409.6789

Beyond blob-ology
Martin T. J. Smith and John L. Rubinstein
(2014) Science 345, 617-9.

Fabrication of carbon films with ~500 nm holes for cryo-EM with a direct detector device.
Chelsea R. Marr, Samir Benlekbir, and John L. Rubinstein
(2013) Journal of Structural Biology 185, 42-7.

Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11 Å resolution.
Samir Benlekbir, Stephanie A. Bueler, and John L. Rubinstein
(2012) Nature Structural and Molecular Biology 19, 1356-62.

The arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM.
Lindsay A. Baker, Ian N. Watt, Michael J. Runswick, John E. Walker, and John L. Rubinstein
(2012) Proceedings of the National Academy of Sciences (USA) 109, 11675-80.

Sub-nanometer resolution structure of the intact T. thermophilus H+-driven ATP synthase.
Wilson Lau and John L. Rubinstein
(2012) Nature 481, 214-8.