Dan Shi, Ph.D.

Dan Shi, Ph.D.

  • Center for Cancer Research
  • National Cancer Institute
  • Center for Structural Biology, 1050 Boyles Street, B469-159
  • Frederick, MD 21702
  • 301-228-4857


I was trained in physics and high resolution electron microscopy (EM) and moved to cryo-electron microscopy (cryo-EM) in 1992. Since then, I have worked on almost every application of cryo-EM in structural biology, from single particles to 3D protein crystals. My work has focused on improving specimen preparation for single particles and protein crystals and on pushing the resolution limit of data collection using cryo-transmission electron microscopy (cryo-TEM) and focused ion beam/scanning electron microscopy (FIB/SEM).  I have also developed new data collection methods and software for electron crystallography.

My research interests include developing new methods and software to push the resolution limit for single particles and protein crystals, and cryo-electron tomography (cryo-ET).     

Areas of Expertise

1) optimizing the electron optics and parameters of cryo-EM to collect atomic resolution data, 2) improving specimen quality for the TEM grids of single particle and protein crystals, 3) electron crystallography - MicroED, 4) understanding the principles and structures of cryo-TEM, FIB/SEM, 5) automation of data collection


Selected Key Publications

Three-dimensional crystals of Ca2+-ATPase from sarcoplasmic recticulum: merging electron diffraction tilt series and imaging the (h,k,0) projection

Shi D, Lewis MR, Young HS, and Stokes DL.
J Mol Biol. 284(5): 1547-64, 1998. [ Journal Article ]

Three-dimensional electron crystallography of protein microcrystals

Shi D, Nannenga BL, Iadanza MG, and Gonen T.
eLife. 2:e01345: 1-17, 2013. [ Journal Article ]

High-resolution structure determination by continuous-rotation data collection in MicroED

Nannenga BL, Shi D, Leslie AGW, and Gonen T.
Nature Methods. 11(9): 927-930, 2014. [ Journal Article ]

Structure of the toxic core of α-synuclein from invisible crystals

Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, and Eisenberg DS.
Nature. 525(7570): 486-490, 2015. [ Journal Article ]

Ion-abrasion scanning electron microscopy reveals surface-connected tubular conduits in HIV-infected macrophages

Bennett AE, Narayan K, Shi D, Hartnell LM, Gousset K, He H, Lowekamp BC, Yoo TS, Bliss D, Freed EO, and Subramaniam S.
PLoS Pathogens. 5(9): e1000591, 2009. [ Journal Article ]