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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
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 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 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
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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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
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
Measurement of atom resolvability in cryo-EM maps with Q-scores
Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a q...
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Article
Open AccessCryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution
Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolut...
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Article
Open AccessCoupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry
The type III CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated genes) systems are bacterially encoded adaptive immune systems for defense against invading nucleic acids. T...
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Article
Convolutional neural networks for automated annotation of cellular cryo-electron tomograms
An algorithm and software tool automating the annotation of subcellular features in cryo-electron tomography data is presented.
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Article
Open AccessVisualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus
Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium Prochlorococc...
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Article
Open AccessErratum: Structural diversity of supercoiled DNA
Nature Communications, 6: Article number: 8440 (2015); Published: 12 October 2015; Updated: 29 October 2015 The original version of this Article contained an error in the spelling of the author Daniel J. Catan...
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Article
Open AccessStructural diversity of supercoiled DNA
By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unkno...
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Article
Open AccessDimeric Organization of Blood Coagulation Factor VIII bound to Lipid Nanotubes
Membrane-bound Factor VIII (FVIII) has a critical function in blood coagulation as the pro-cofactor to the serine-protease Factor IXa (FIXa) in the FVIIIa-FIXa complex assembled on the activated platelet membr...
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Article
Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages
Equip** an electron microscope with Zernike phase-contrast optics dramatically increases the contrast of the images. Dai et al. describe how to successfully apply this technology for the acquisition and analysi...
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Article
Open AccessAn atomic model of brome mosaic virus using direct electron detection and real-space optimization
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bi...
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Article
Visualizing virus assembly intermediates inside marine cyanobacteria
This study reports the first application of Zernike phase contrast (ZPC) electron cryo-tomography to examine cellular processes without the need for labelling or sectioning; the technique is used to visualize ...
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Chapter
Principles of Virus Structural Organization
Viruses, the molecular nanomachines infecting hosts ranging from prokaryotes to eukaryotes, come in different sizes, shapes, and symmetries. Questions such as what principles govern their structural organizati...
