Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
Xueming Li,Paul Mooney,Shawn Q. Zheng,Shawn Q. Zheng,Christopher R. Booth,Michael B. Braunfeld,Michael B. Braunfeld,Sander Gubbens,David A. Agard,David A. Agard,Yifan Cheng +10 more
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TLDR
This approach determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density and greatly enhances image quality and data acquisition efficiency.Abstract:
In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 A). Using this approach, we determined a 3.3-A-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.read more
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Benchmarking cryo-EM Single Particle Analysis Workflow.
Laura Y. Kim,William J. Rice,Edward T. Eng,Mykhailo Kopylov,Anchi Cheng,Ashleigh M. Raczkowski,Kelsey D. Jordan,Daija Bobe,Clinton S. Potter,Bridget Carragher +9 more
TL;DR: It is believed it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis, to provide confidence that all aspects of the pipeline are capable of producing maps to high resolution.
Journal ArticleDOI
Folding and insertion thermodynamics of the transmembrane WALP peptide
TL;DR: Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence, hinting at cooperative physics beyond the residue level.
Journal ArticleDOI
Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition.
TL;DR: Tensor singular value decomposition (SVD) is a method to find a low-dimensional representation of data with meaningful structure in three or more dimensions that improves both convergent beam electron diffraction patterns and virtual-aperture annular dark field images.
Journal ArticleDOI
Structural basis for the adsorption of a single-stranded RNA bacteriophage
Ran Meng,Mengqiu Jiang,Zhicheng Cui,Jeng-Yih Chang,Kailu Yang,Kailu Yang,Joanita Jakana,Xinzhe Yu,Zhao Wang,Bo Hu,Junjie Zhang +10 more
TL;DR: Structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus are presented, showing a network of hydrophobic and electrostatic interactions at the Mat- pilus interface, providing insights into the F-like type IV secretion systems.
Journal ArticleDOI
Structure of human Aichi virus and implications for receptor binding.
Ling Zhu,Xiangxi Wang,Jingshan Ren,Abhay Kotecha,Thomas S. Walter,Shuai Yuan,Teruo Yamashita,Tobias J. Tuthill,Elizabeth E. Fry,Zihe Rao,Zihe Rao,David I. Stuart +11 more
TL;DR: This first high-resolution structure for a kobuvirus is intermediate between those of the enteroviruses and cardioviruses, with a shallow, narrow depression bounded by the prominent VP0 CD loops, replacing the depression known as the canyon, frequently the site of receptor attachment in enterovirus.
References
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Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution.
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Accurate determination of local defocus and specimen tilt in electron microscopy
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Prevention of overfitting in cryo-EM structure determination
Sjors H.W. Scheres,Shaoxia Chen +1 more
TL;DR: Analysis of simulated data with realistic signal-to-noise ratios indicates that the accuracy of the orientation determination is not affected by the exclusion of high-frequency terms, nor by the use of a model that is reconstructed from only half of the particles, as expected.