Noteworthy Results

This page highlights some of the most noteworthy results from the NCMI team. See the publications page for a more complete list of the center's published research.

Accurate model annotation of a near-atomic resolution cryo-EM map - March 2017
A 3.3 Å cryo-EM structure of a bacterial virus (P22 phage) was determined. This structure reveals the chemical basis for virus stability. This study also developed a rigours protocol to validate the structure model derived from cryo-EM map. DOI:10.1073/pnas.1621152114
See also: Cryo-Electron Microscopy Achieves Unprecedented Resolution Using New Computational Methods - Berkeley Lab

The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase Vo Proton Channel - March 2018
A 3.5 Å cryo-EM map of the membrane-spanning region of a yeast proton pump (V0ATPase), consisting of 15 polypeptide subunits. The analysis of the structure led to the discovery of a new protein in this complex which was validated by subsequent biochemical and genetic analysis The spatial disposition of these subunits suggest a mechanism for the hydrogen ion transport across the membrane. DOI:10.1016/j.molcel.2018.02.006

Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM - August 2017
A 3.5 Å cryo-EM structure of bacterial chaperonin GroEL was determined. A 3-D focused classification of each subunit from each GroEL particle image led to revelation that there are three dominant conformations of GroEL subunits. The conformational differences stem from the orientations of the apical domain of the subunit. Each of these conformations can be found to correspond to a distinct  PDB structure determined by X-ray crystallography. We found that virtually every one of the 14 chemically identical subunits of every particle has the potential to have any of these conformations. This study shows the feasibility of using cryo-EM to reveal structure dynamics within a single protein oligomer. DOI: 10.1073/pnas.1704725114

Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach - March 2018
A 9 Å cryo-EM map of a small (30 kDa) RNA portion of the HIV genome, with an atomic model fitted into it. This structure was validated with two data sets from different electron microscopes and direct electron detectors. The analysis of the cryo-EM map was a collaboration with an NMR spectroscopist and a computational biologist. The structure revealed a superhelical twist of the dimeric RNA and a flipped-out base within a conserved purine-rich bulge. DOI:10.1016/j.str.2018.01.001

Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly - February 2018
Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC). We determined a 5.8 Å cryo-EM structure of the eNP NC-like assembly from which we identified a new regulatory role for eNP helices alpha22-alpha23. Our structure inspired follow-up biochemical analysis which suggests that the N terminus and alpha22-alpha23 of eNP function as context-dependent regulatory modules (CDRMs). Our current study provides a framework for a structural mechanism for NC-like assembly and a new therapeutic target. DOI: 10.1016/j.cell.2018.02.009

Convolutional neural networks for automated annotation of cellular cryo-electron tomograms
- August 2017
Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package. DOI: 10.1038/nmeth.4405
See also: Method speeds up time to analyze complex microscopic images -

Electron cryotomography reveals ultrastructure alterations in platelets from patients with ovarian cancer - November 2015
Cryo-electron tomography was carried out for platelets derived from the blood of normal subjects and patients diagnosed with ovarian cancer. In contrast with platelets from healthy subjects, their normally continuous circular ring of microtubules is broken, disrupted, and shorter in ovarian cancer patients. DOI:10.1073/pnas.1518628112