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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Retrieving functional pathways of biomolecules from single-particle snapshots.
Ali Dashti,Ghoncheh Mashayekhi,Mrinal Shekhar,Mrinal Shekhar,Danya Ben Hail,Salah Salah,Salah Salah,Peter Schwander,Amedee des Georges,Amedee des Georges,Abhishek Singharoy,Joachim Frank,Abbas Ourmazd +12 more
TL;DR: In this article, the authors presented chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands.
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Fundamental Limits in Multi-Image Alignment
TL;DR: This work derives and analyzes the Cramér-Rao and Ziv-Zakai lower bounds under different statistical models for the underlying image, and shows the existence of different behavior zones depending on the difficulty level of the problem, given by the SNR conditions of the input images.
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Structure of an endogenous yeast 26S proteasome reveals two major conformational states
Bai Luan,Xiuliang Huang,Jianping Wu,Ziqing Mei,Yiwei Wang,Xiaobin Xue,Chuangye Yan,Jiawei Wang,Daniel Finley,Yigong Shi,Feng Wang +10 more
TL;DR: Cryo-EM structures of the endogenous 26S proteasome from Saccharomyces cerevisiae reveal two distinct conformational states, which appear to correspond to different states of ATP hydrolysis and substrate binding, and serve as a molecular basis for mechanistic understanding of proteAsome function.
Journal ArticleDOI
Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1–Npl4
Nicholas O. Bodnar,Kelly H. Kim,Zhejian Ji,Thomas E. Wales,Vladimir Svetlov,Evgeny Nudler,John R. Engen,Thomas Walz,Tom A. Rapoport +8 more
TL;DR: The results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.
Journal ArticleDOI
CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilus.
Nicole Poweleit,Peng Ge,Hong Hanh Nguyen,Rachel R. Ogorzalek Loo,Robert P. Gunsalus,Z. Hong Zhou +5 more
TL;DR: The structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification, which explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation.
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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Prevention of overfitting in cryo-EM structure determination
Sjors H.W. Scheres,Shaoxia Chen +1 more
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