CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou,Nikolaus Grigorieff +1 more
TLDR
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.About:
This article is published in Journal of Structural Biology.The article was published on 2015-11-01 and is currently open access. It has received 3512 citations till now. The article focuses on the topics: Contrast transfer function.read more
Citations
More filters
Journal ArticleDOI
New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov,Takanori Nakane,Björn O. Forsberg,Dari Kimanius,Wim J. H. Hagen,Erik Lindahl,Erik Lindahl,Sjors H.W. Scheres +7 more
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.
Journal ArticleDOI
Gctf: Real-time CTF determination and correction
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.
Journal ArticleDOI
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Christopher O. Barnes,Claudia A. Jette,Morgan E. Abernathy,Kim Marie A. Dam,Shannon R. Esswein,Harry B. Gristick,Andrey G. Malyutin,Naima G. Sharaf,Kathryn E. Huey-Tubman,Yu E. Lee,Davide F. Robbiani,Davide F. Robbiani,Michel C. Nussenzweig,Michel C. Nussenzweig,Anthony P. West,Pamela J. Bjorkman +15 more
TL;DR: Eight new structures of distinct COVID-19 human neutralizing antibodies 5 in complex with the SARS-CoV-2 spike trimer or RBD are solved and rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use are provided.
Journal ArticleDOI
Distinct conformational states of SARS-CoV-2 spike protein
Yongfei Cai,Yongfei Cai,Jun Zhang,Jun Zhang,Tianshu Xiao,Tianshu Xiao,Hanqin Peng,Sarah M. Sterling,Richard M. Walsh,Shaun Rawson,Sophia Rits-Volloch,Bing Chen,Bing Chen +12 more
TL;DR: Two cryo–electron microscopy structures derived from a preparation of the full-length S protein, representing its prefusion and postfusion conformations, are reported, advancing the understanding of SARS-CoV-2 entry and may guide the development of vaccines and therapeutics.
Journal ArticleDOI
Structures and distributions of SARS-CoV-2 spike proteins on intact virions.
Zunlong Ke,Joaquín Otón,Kun Qu,Mirko Cortese,Vojtech Zila,Lesley McKeane,Takanori Nakane,Jasenko Zivanov,Christopher J. Neufeldt,Berati Cerikan,John M. Lu,Julia Peukes,Xiaoli Xiong,Hans-Georg Kräusslich,Sjors H.W. Scheres,Ralf Bartenschlager,Ralf Bartenschlager,John A. G. Briggs +17 more
TL;DR: Cryo-electron microscopy and tomography is applied to image intact SARS-CoV-2 virions, determining the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface and providing a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.
References
More filters
Journal ArticleDOI
Accurate determination of local defocus and specimen tilt in electron microscopy
TL;DR: Two computer programs are presented, CTFFIND3 and CTFTILT, which determine defocus parameters from images of untilted specimens, as well as defocus and tilt parameters from image of tilted specimens, respectively, using a simple algorithm.
Journal ArticleDOI
A new generation of the IMAGIC image processing system.
TL;DR: IMAGIC's novel angular reconstitution approach allows for the rapid determination of three-dimensional structures of uncrystallized molecules to high resolution.
Journal ArticleDOI
Single-particle electron cryo-microscopy: towards atomic resolution.
M. van Heel,Brent E. Gowen,Rishi Matadeen,Elena V. Orlova,Robert D. Finn,Tillmann Pape,D. Cohen,Holger Stark,Ralf Schmidt,Michael Schatz,Ardan Patwardhan +10 more
TL;DR: Electron microscopy is a very direct method of structure determination that complements the well-established techniques of X-ray crystallography and NMR spectroscopy and is established itself as an important – still upcoming – technique for studying the structures of large biological macromolecules.
Journal ArticleDOI
A primer to single-particle cryo-electron microscopy.
TL;DR: This primer explains the different steps and considerations involved in structure determination by single-particle cryo-EM to provide an overview for scientists wishing to understand more about this technique and the interpretation of data obtained with it, as well as a starting guide for new practitioners.
Journal ArticleDOI
Volta potential phase plate for in-focus phase contrast transmission electron microscopy
TL;DR: The Volta phase plate has a long service life and has been used for more than 6 mo without noticeable degradation in performance, and the mechanism underlying the VPP is the same as the one responsible for the degradation over time of the performance of thin-film Zernike phase plates, but in the V PP it is used in a constructive way.