Gctf: Real-time CTF determination and correction

doi:10.1016/J.JSB.2015.11.003

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Gctf: Real-time CTF determination and correction

Journal Article•DOI•

Gctf: Real-time CTF determination and correction

Kai Zhang¹•Institutions (1)

Laboratory of Molecular Biology¹

01 Jan 2016-Journal of Structural Biology (J Struct Biol)-Vol. 193, Iss: 1, pp 1-12

TL;DR: The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra of observed micrographs after background subtraction to improve CTF parameters of all particles for subsequent image processing.

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About: This article is published in Journal of Structural Biology.The article was published on 2016-01-01 and is currently open access. It has received 2919 citations till now. The article focuses on the topics: Background subtraction.

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Journal Article•DOI•

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

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Ali Punjani¹, John L. Rubinstein, David J. Fleet¹, Marcus A. Brubaker²•Institutions (2)

University of Toronto¹, York University²

01 Mar 2017-Nature Methods

TL;DR: It is shown that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer.

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Abstract: Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).

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4,342 citations

Journal Article•DOI•

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.

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Renhong Yan¹, Yuanyuan Zhang¹, Yaning Li², Lu Xia¹, Yingying Guo¹, Qiang Zhou¹ - Show less +2 more•Institutions (2)

Westlake University¹, Tsinghua University²

04 Mar 2020-Science

TL;DR: Cryo–electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B0AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein of SARS-CoV-2 are presented, providing important insights into the molecular basis for coronavirus recognition and infection.

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Abstract: Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and the new coronavirus (SARS-CoV-2) that is causing the serious coronavirus disease 2019 (COVID-19) epidemic. Here, we present cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B0AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 angstroms at the ACE2-RBD interface. The ACE2-B0AT1 complex is assembled as a dimer of heterodimers, with the collectrin-like domain of ACE2 mediating homodimerization. The RBD is recognized by the extracellular peptidase domain of ACE2 mainly through polar residues. These findings provide important insights into the molecular basis for coronavirus recognition and infection.

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4,109 citations

Journal Article•DOI•

New tools for automated high-resolution cryo-EM structure determination in RELION-3.

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Jasenko Zivanov¹, Takanori Nakane¹, Björn O. Forsberg², Dari Kimanius², Wim J. H. Hagen, Erik Lindahl², Erik Lindahl³, Sjors H.W. Scheres¹ - Show less +4 more•Institutions (3)

Laboratory of Molecular Biology¹, Science for Life Laboratory², Royal Institute of Technology³

09 Nov 2018-eLife

TL;DR: CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations in the third major release of RELION.

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Abstract: Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 A compared to previous RELION versions.

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3,520 citations

Cites methods from "Gctf: Real-time CTF determination a..."

...Using default parameters, the script launched motion correction of the 1255 40-frame movies in our own implementation of the MotionCor2 algorithm, and estimated CTF parameters in Gctf (Zhang, 2016)....
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...Using default parameters, we performed motion correction of the 2,925 16frame movies in our own implementation of the MotionCor2 algorithm, and estimated CTF parameters in gCTF [Zhang, 2016]....
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...Therefore, in practice it would probably be faster to start from defoci provided by local CTF estimation programs, such as ctftilt [Mindell and Grigorie↵, 2003], gctf [Zhang, 2016] or Warp [Tegunov and Cramer, 2018]....
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...Using default parameters, the script launched motion correction of the 1,255 40-frame movies in our own implementation of the MotionCor2 algorithm, and estimated CTF parameters in gCTF [Zhang, 2016]....
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...In RELION, per-micrograph CTF parameters are determined through wrappers to CTFFIND (Rohou and Grigorieff, 2015) or Gctf (Zhang, 2016)....
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Journal Article•DOI•

Cryo-EM structures of tau filaments from Alzheimer’s disease

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Anthony W. P. Fitzpatrick¹, Benjamin Falcon¹, Shaoda He¹, Alexey G. Murzin¹, Garib N. Murshudov¹, Holly J. Garringer², R. Anthony Crowther¹, Bernardino Ghetti², Michel Goedert¹, Sjors H.W. Scheres¹ - Show less +6 more•Institutions (2)

Laboratory of Molecular Biology¹, Indiana University²

05 Jul 2017-Nature

TL;DR: Scheres et al. as mentioned in this paper presented a 3.4-3.5-resolution image of the brain of an individual with Alzheimer's disease and showed that the protein cores are made of two identical protofilaments comprising residues 306-378 of tau protein.

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Abstract: Alzheimer’s disease is the most common neurodegenerative disease, and there are no mechanism-based therapies. The disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex. Neurofibrillary lesions comprise paired helical and straight tau filaments, whereas tau filaments with different morphologies characterize other neurodegenerative diseases. No high-resolution structures of tau filaments are available. Here we present cryo-electron microscopy (cryo-EM) maps at 3.4–3.5 A resolution and corresponding atomic models of paired helical and straight filaments from the brain of an individual with Alzheimer’s disease. Filament cores are made of two identical protofilaments comprising residues 306–378 of tau protein, which adopt a combined cross-β/β-helix structure and define the seed for tau aggregation. Paired helical and straight filaments differ in their inter-protofilament packing, showing that they are ultrastructural polymorphs. These findings demonstrate that cryo-EM allows atomic characterization of amyloid filaments from patient-derived material, and pave the way for investigation of a range of neurodegenerative diseases. High-resolution structures of tau filaments shed light on the ultrastructure of neurofibrillary lesions in Alzheimer’s disease. Alzheimer's disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex. The lesions are made of paired helical and straight tau filaments (PHFs and SFs, respectively). Different tau filaments characterize other neurodegenerative diseases, suggesting that molecular conformers of aggregated tau underlie human tauopathies. No high-resolution structures of tau filaments are currently available. Here, Sjors Scheres and colleagues present cryo-electron microscopy (cryo-EM) maps at 3.5 A resolution and corresponding atomic models of PHFs and SFs from the brain of an individual with Alzheimer's disease. Their results show that cryo-EM enables atomic characterization of amyloid filaments from patient-derived material and could be used to study a range of neurodegenerative diseases.

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1,265 citations

Journal Article•DOI•

A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2.

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Chi Xiangyang¹, Renhong Yan², Jun Zhang¹, Zhang Guanying¹, Yuanyuan Zhang², Hao Meng¹, Zhe Zhang¹, Pengfei Fan¹, Dong Yunzhu¹, Yilong Yang¹, Chen Zhengshan¹, Yingying Guo², Jinlong Zhang¹, Yaning Li³, Xiaohong Song¹, Chen Yi¹, Lu Xia², Ling Fu¹, Lihua Hou¹, Junjie Xu¹, Changming Yu¹, Jianmin Li¹, Qiang Zhou², Wei Chen¹ - Show less +20 more•Institutions (3)

Academy of Military Medical Sciences¹, Westlake University², Tsinghua University³

22 Jun 2020-Science

TL;DR: The epitope of 4A8 is defined as the N-terminal domain (NTD) of the S protein by determining with cryo–eletron microscopy its structure in complex with the Sprotein, which points to the NTD as a promising target for therapeutic mAbs against COVID-19.

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Abstract: Developing therapeutics against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be guided by the distribution of epitopes, not only on the receptor binding domain (RBD) of the Spike (S) protein but also across the full Spike (S) protein We isolated and characterized monoclonal antibodies (mAbs) from 10 convalescent COVID-19 patients Three mAbs showed neutralizing activities against authentic SARS-CoV-2 One mAb, named 4A8, exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-2 but does not bind the RBD We defined the epitope of 4A8 as the N-terminal domain (NTD) of the S protein by determining with cryo-eletron microscopy its structure in complex with the S protein to an overall resolution of 31 angstroms and local resolution of 33 angstroms for the 4A8-NTD interface This points to the NTD as a promising target for therapeutic mAbs against COVID-19

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1,189 citations

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References

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Journal Article•DOI•

RELION: implementation of a Bayesian approach to cryo-EM structure determination.

[...]

Sjors H.W. Scheres¹•Institutions (1)

Laboratory of Molecular Biology¹

01 Dec 2012-Journal of Structural Biology

TL;DR: Developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined are described.

...read moreread less

4,554 citations

"Gctf: Real-time CTF determination a..." refers methods in this paper

...The program is fully compatible with Relion (Scheres, 2012) and the log files and output STAR files can be directly used for further 2D or 3D classification....
[...]
...Gctf is an independent program and the outputs can be easily imported into other cryoEM software such as Relion (Scheres, 2012) and Frealign (Grigorieff, 2007)....
[...]

Journal Article•DOI•

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.

[...]

Alexis Rohou¹, Nikolaus Grigorieff¹•Institutions (1)

Howard Hughes Medical Institute¹

01 Nov 2015-Journal of Structural Biology

TL;DR: Modifications to the CTFFIND algorithm are described which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates.

...read moreread less

3,512 citations

"Gctf: Real-time CTF determination a..." refers methods in this paper

...Speed comparison was done with CTFFIND3 (Mindell and Grigorieff, 2003), CTFFIND4 (Rohou and Grigorieff, 2015), FASTDEF (Vargas et al....
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Journal Article•DOI•

EMAN2: an extensible image processing suite for electron microscopy.

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Guang Tang¹, Liwei Peng¹, Philip R. Baldwin², Deepinder S. Mann¹, Wen Jiang³, I. Rees¹, Steven J. Ludtke¹ - Show less +3 more•Institutions (3)

Baylor College of Medicine¹, University of Texas Health Science Center at Houston², Purdue University³

01 Jan 2007-Journal of Structural Biology

TL;DR: EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1.

...read moreread less

2,852 citations

"Gctf: Real-time CTF determination a..." refers background or methods in this paper

...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al....
[...]
...There are currently several programs available for CTF determination (Ludtke et al., 1999; Mallick et al., 2005; Mindell and Grigorieff, 2003; Penczek et al., 2014; Shaikh et al., 2008; Sorzano et al., 2004; Tang et al., 2007; Vargas et al., 2013; Voortman et al., 2011)....
[...]
...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al., 2008) and Xmipp (Sorzano et al., 2004) etc....
[...]

Journal Article•DOI•

EMAN: semiautomated software for high-resolution single-particle reconstructions.

[...]

Steven J. Ludtke, Philip R. Baldwin¹, Wah Chiu¹•Institutions (1)

Baylor College of Medicine¹

01 Dec 1999-Journal of Structural Biology

TL;DR: EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs, was written from scratch in C++ and is provided free of charge on the Web site.

...read moreread less

2,551 citations

"Gctf: Real-time CTF determination a..." refers background or methods in this paper

...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al....
[...]
...There are currently several programs available for CTF determination (Ludtke et al., 1999; Mallick et al., 2005; Mindell and Grigorieff, 2003; Penczek et al., 2014; Shaikh et al., 2008; Sorzano et al., 2004; Tang et al., 2007; Vargas et al., 2013; Voortman et al., 2011)....
[...]
...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al., 2008) and Xmipp (Sorzano et al., 2004) etc....
[...]

Journal Article•DOI•

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM

[...]

Xueming Li¹, Paul Mooney, Shawn Q. Zheng², Shawn Q. Zheng¹, Christopher R. Booth, Michael B. Braunfeld¹, Michael B. Braunfeld², Sander Gubbens, David A. Agard², David A. Agard¹, Yifan Cheng¹ - Show less +7 more•Institutions (2)

University of California, San Francisco¹, Howard Hughes Medical Institute²

01 Jun 2013-Nature Methods

TL;DR: 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.

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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 moreread less

1,726 citations

"Gctf: Real-time CTF determination a..." refers background in this paper

...Beam induced movement correction using movies has greatly improved the resolution of the final reconstruction (Bai et al., 2013; Li et al., 2013)....
[...]