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Article
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryogenic electron microscopy (cryo-EM) ...
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Article
Open AccessHub stability in the calcium calmodulin-dependent protein kinase II
The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoform...
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Article
Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models
Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian mixture m...
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Article
Open AccessTargeted mutagenesis of the herpesvirus fusogen central helix captures transition states
Herpesviruses remain a burden for animal and human health, including the medically important varicella-zoster virus (VZV). Membrane fusion mediated by conserved core glycoproteins, the fusogen gB and the heter...
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Article
Open AccessStructural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans
Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the stru...
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Article
Open AccessPreviously uncharacterized rectangular bacterial structures in the dolphin mouth
Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining reveale...
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Article
Open AccessCryoET reveals organelle phenotypes in huntington disease patient iPSC-derived and mouse primary neurons
Huntington’s disease (HD) is caused by an expanded CAG repeat in the huntingtin gene, yielding a Huntingtin protein with an expanded polyglutamine tract. While experiments with patient-derived induced pluripot...
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Article
Open Access3D RNA-scaffolded wireframe origami
Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique ...
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Protocol
Near-Atomic Resolution Cryo-EM Image Reconstruction of RNA
The rapid development of cryogenic electron microscopy (cryo-EM) enables the structure determination of macromolecules without the need for crystallization. Protein, protein–lipid, and protein–nucleic acid com...
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Article
Open AccessElectron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biolog...
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Article
Chikungunya virus assembly and budding visualized in situ using cryogenic electron tomography
Chikungunya virus (CHIKV) is a representative alphavirus causing debilitating arthritogenic disease in humans. Alphavirus particles assemble into two icosahedral layers: the glycoprotein spike shell embedded i...
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Protocol
Methods and Applications of Campenot Trichamber Neuronal Cultures for the Study of Neuroinvasive Viruses
The development of compartmentalized neuron culture systems has been invaluable in the study of neuroinvasive viruses, including the alpha herpesviruses Herpes Simplex Virus 1 (HSV-1) and Pseudorabies Virus (P...
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Article
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology
Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressi...
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Article
Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome
Drug discovery campaigns against COVID-19 are beginning to target the SARS-CoV-2 RNA genome. The highly conserved frameshift stimulation element (FSE), required for balanced expression of viral proteins, is a ...
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Article
Open AccessCryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin
Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which ...
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Article
Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution
Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1–3. However, cryo-EM studies of protein-free RNA are in their early ...
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Article
Open AccessCryo-electron tomography provides topological insights into mutant huntingtin exon 1 and polyQ aggregates
Huntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentou...
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Article
Open AccessCryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeli...
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Article
Open AccessResolving individual atoms of protein complex by cryo-electron microscopy
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Article
3D RNA nanocage for encapsulation and shielding of hydrophobic biomolecules to improve the in vivo biodistribution
Ribonucleic acid (RNA) nanotechnology platforms have the potential of harboring therapeutics for in vivo delivery in disease treatment. However, the nonspecific interaction between the harbored hydrophobic drugs ...
