Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN

LF Kinman, BM Powell, ED Zhong, B Berger… - Nature protocols, 2023 - nature.com
Single-particle cryogenic electron microscopy (cryo-EM) has emerged as a powerful
technique to visualize the structural landscape sampled by a protein complex. However …

Critical steps in the assembly process of the bacterial 50S ribosomal subunit

A Seffouh, R Nikolay, J Ortega - Nucleic Acids Research, 2024 - academic.oup.com
During assembly, ribosomal particles in bacteria fold according to energy landscapes
comprised of multiple parallel pathways. Cryo-electron microscopy studies have identified a …

Assembly landscape for the bacterial large ribosomal subunit

K Sheng, N Li, JN Rabuck-Gibbons, X Dong… - Nature …, 2023 - nature.com
Assembly of ribosomes in bacteria is highly efficient, taking~ 2-3 min, but this makes the
abundance of assembly intermediates very low, which is a challenge for mechanistic …

Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN

BM Powell, JH Davis - Nature Methods, 2024 - nature.com
Cryo-electron tomography (cryo-ET) enables observation of macromolecular complexes in
their native, spatially contextualized cellular environment. Cryo-ET processing software to …

A proteolytic AAA+ machine poised to unfold protein substrates

A Ghanbarpour, RT Sauer, JH Davis - Nature communications, 2024 - nature.com
AAA+ proteolytic machines unfold proteins before degrading them. Here, we present cryoEM
structures of ClpXP-substrate complexes that reveal a postulated but heretofore unseen …

A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation

A Ghanbarpour, SE Cohen, X Fei, LF Kinman… - Nature …, 2023 - nature.com
AAA+ proteases degrade intracellular proteins in a highly specific manner. E. coli ClpXP, for
example, relies on a C-terminal ssrA tag or other terminal degron sequences to recognize …

An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins

A Ghanbarpour, B Telusma, BM Powell, JJ Zhang… - …, 2024 - pmc.ncbi.nlm.nih.gov
FtsH, a AAA protease, associates with HflK/C subunits to form a megadalton complex that
spans the inner membrane and extends into the periplasm of E. coli. How this complex and …

Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome

BR Warner, K Fredrick - RNA, 2024 - rnajournal.cshlp.org
30S subunits become inactive upon exposure to low Mg2+ concentration, because of a
reversible conformational change that entails nucleotides (nt) in the neck helix (h28) and 3 …

[HTML][HTML] Imaging structurally dynamic ribosomes with cryogenic electron microscopy

SM Webster, MB May, BM Powell, JH Davis - ArXiv, 2023 - ncbi.nlm.nih.gov
Throughout the history of electron microscopy, ribosomes have served as an ideal subject
for imaging and technological development, which in turn has driven our understanding of …

[HTML][HTML] Rapid structural analysis of bacterial ribosomes in situ

BM Powell, TS Brant, JH Davis, S Mosalaganti - bioRxiv, 2024 - ncbi.nlm.nih.gov
Rapid structural analysis of purified proteins and their complexes has become increasingly
common thanks to key methodological advances in cryo-electron microscopy (cryo-EM) and …