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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Structural basis of αE-catenin-F-actin catch bond behavior
Xiao-Ping Xu,Sabine Pokutta,Miguel A. Torres,Mark F. Swift,Dorit Hanein,Niels Volkmann,William I. Weis +6 more
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Motion-corrected Fourier ptychography
TL;DR: A novel FP reconstruction method to efficiently correct for unknown sample motion by adaptively update the sample's Fourier spectrum from low spatial-frequency regions towards high spatial- frequency ones, with an additional motion recovery and phase-offset compensation procedure for each sub-spectrum.
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Correction: Structural basis for the prion-like MAVS filaments in antiviral innate immunity.
Hui Xu,Xiaojing He,Hui Zheng,Lily Jun Shen Huang,Fajian Hou,Zhiheng Yu,Michael Jason de la Cruz,Brian Borkowski,Xuewu Zhang,Zhijian J. Chen,Qiu-Xing Jiang +10 more
TL;DR: The new model shows that the MAVS CARD filament exhibits a C1 helical symmetry in agreement with Wu et al. (2014), which suggested that the helical ambiguity in helical reconstruction was not fully resolved in the previous analysis.
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A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.
TL;DR: A new protocol to create initial models using I-TASSER protein structure prediction, followed by EM density map-based rigid-body structure fitting, flexible fragment adjustment and atomic-level structure refinement simulations, which demonstrates a new avenue that is ready to use for large-scale cryo-EM-based structure modeling and Atomic-level densityMap-guided structure refinement.
References
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Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution.
TL;DR: The three-dimensional structure of the proteasome from the archaebacterium Thermoplasma acidophilum has been elucidated by x-ray crystallographic analysis by means of isomorphous replacement and cyclic averaging.
Journal ArticleDOI
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Journal ArticleDOI
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.