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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Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core.
Andrew J. Borst,Connor Weidle,Gray,Brandon Frenz,Joost Snijder,Michael Gordon Joyce,Ivelin S. Georgiev,Guillaume Stewart-Jones,Peter D. Kwong,Andrew T. McGuire,Frank DiMaio,Leonidas Stamatatos,Leonidas Stamatatos,Marie Pancera,Marie Pancera,David Veesler +15 more
TL;DR: Results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1–3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former.
Journal ArticleDOI
Cryo-electron microscopy structure of the glucagon receptor with a dual-agonist peptide
Rulue Chang,Xin Zhang,Anna Qiao,Antao Dai,Matthew J. Belousoff,Qiuxiang Tan,Lijun Shao,Lijun Shao,Li Zhong,Guangyao Lin,Guangyao Lin,Yi Lynn Liang,Limin Ma,Shuo Han,Dehua Yang,Radostin Danev,Ming-Wei Wang,Denise Wootten,Beili Wu,Beili Wu,Patrick M. Sexton +20 more
TL;DR: Cryo-EM is used to solve the structure of an active P15-GCGR-Gs complex and it is revealed that P15 has a reduced interaction with the first extracellular loop (ECL1) and the top of transmembrane segment 1 (TM1) such that there is increased mobility of the GCGRextracellular domain and at the C terminus of the peptide compared with the GCG-bound receptor.
Journal ArticleDOI
Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps †.
Todor K. Avramov,Daniel L Vyenielo,Josué Gómez-Blanco,Swathi Adinarayanan,Javier Vargas,Dong Si +5 more
TL;DR: In this article, the authors proposed supervised deep learning methods to extract representative 3D features at high, medium and low resolutions from simulated protein density maps and build classification models that objectively validate resolutions of experimental 3D cryo-EM maps.
Journal ArticleDOI
Cryo-EM structure of the ASIC1a-mambalgin-1 complex reveals that the peptide toxin mambalgin-1 inhibits acid-sensing ion channels through an unusual allosteric effect.
Demeng Sun,You Yu,Xiaobin Xue,Man Pan,Ming Wen,Siyu Li,Qian Qu,Xiaorun Li,Longhua Zhang,Xueming Li,Lei Liu,Maojun Yang,Changlin Tian +12 more
TL;DR: The structure provides the first experimental evidence that mambalgin-1 interacts directly with the extracellular thumb domain of cASIC1a, rather than inserting into the acid-sensing pocket, as previously reported and provides crucial insights for the development of new optimized inhibitors of ASICs.
Journal ArticleDOI
The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services
TL;DR: A technical description of the Dynamo software package for subtomogram averaging is provided and details are given on advanced MATLAB libraries, parallelization strategies, the use of GPUs and accessibility though the Amazon cloud computing services.
References
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