We thank W. Liu for assistance in molecular dynamic flexible fitting. This research has been supported in part by grants from the National Key R&D Program of China (2017YFA0505300 and 2016YFA0400900) and the US National Institutes of Health (GM071940/DE025567/DE028583/AI094386). We acknowledge the use of instruments at the Electron Imaging Center for Nanomachines supported by UCLA and by instrumentation grants from NIH (1S10RR23057 and 1U24GM116792) and NSF (DBI-1338135 and DMR-1548924). We thank the Bioinformatics Center of the University of Science and Technology of China, School of Life Science, for providing supercomputing resources for this project.

Reviewer information

Nature thanks Sarah Butcher, Venigalla Rao and the other anonymous reviewer(s) for their contribution to the peer review of this work.