Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION -3.1

IUCrJ
Jasenko ZivanovSjors Hw Scheres

Abstract

Methods are presented that detect three types of aberrations in single-particle cryo-EM data sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy. Because these methods only depend on the availability of a preliminary 3D reconstruction from the data, they can be used to correct for these aberrations for any given cryo-EM data set, a posteriori. Using five publicly available data sets, it is shown that considering these aberrations improves the resolution of the 3D reconstruction when these effects are present. The methods are implemented in version 3.1 of the open-source software package RELION.

References

Sep 22, 2000·Ultramicroscopy·W O Saxton
Jun 5, 2003·Journal of Structural Biology·Joseph A Mindell, Nikolaus Grigorieff
Dec 7, 2007·Ultramicroscopy·O L KrivanekJ W Woodruff
Dec 21, 2013·Methods in Molecular Biology·Fei Guo, Wen Jiang
Oct 22, 2014·Proceedings of the National Academy of Sciences of the United States of America·Radostin DanevWolfgang Baumeister
Aug 19, 2015·Journal of Structural Biology·Timothy Grant, Nikolaus Grigorieff
Mar 8, 2016·ELife·Radostin Danev, Wolfgang Baumeister
Apr 14, 2016·Nature Methods·Andrii IudinArdan Patwardhan
Sep 16, 2016·Nature·Rafael Fernandez-Leiro, Sjors H W Scheres
Jan 22, 2017·ELife·Radostin DanevWolfgang Baumeister
Jun 6, 2017·Acta Crystallographica. Section D, Structural Biology·Daniel K ClarePeijun Zhang
Oct 11, 2017·Nature Methods·Mark A HerzikGabriel C Lander
Jun 29, 2018·Frontiers in Molecular Biosciences·Laura Y KimBridget Carragher
May 13, 2019·Trends in Biochemical Sciences·Radostin DanevMasahide Kikkawa
Nov 12, 2019·IUCrJ·K NaydenovaC J Russo

❮ Previous
Next ❯

Citations

Aug 28, 2020·ELife·Yiming NiuRoderick MacKinnon
Aug 29, 2020·Proceedings of the National Academy of Sciences of the United States of America·Basil J GreberEva Nogales
Aug 2, 2020·Nature Structural & Molecular Biology·Xiaoli XiongJohn A G Briggs
Jul 19, 2020·Proceedings of the National Academy of Sciences of the United States of America·Xia YaoNieng Yan
Aug 30, 2020·Nature Communications·Jonathan A FloresSteve L Reichow
Sep 12, 2020·Science·Joshua A BoyerQi Zhang
Aug 5, 2020·Nature Structural & Molecular Biology·Daniel N Grba, Judy Hirst
Mar 4, 2020·Nature·Amber Dance
Sep 18, 2020·ELife·Matthew D LauverAron E Lukacher
Oct 11, 2020·Nature Communications·Ricardo D RighettoHenning Stahlberg
Nov 13, 2020·Nature Communications·Markus StabrinStefan Raunser
Nov 20, 2020·IUCrJ·Jennifer N CashMichael A Cianfrocco
Dec 19, 2020·Proceedings of the National Academy of Sciences of the United States of America·Kefang LiuGeorge Fu Gao
Dec 20, 2020·Nature Communications·Tomáš KoubaLibor Krásný
Jan 2, 2021·Proceedings of the National Academy of Sciences of the United States of America·B David PerssonNiklas Arnberg
Feb 6, 2021·Nature Methods·Ellen D ZhongJoseph H Davis
Oct 23, 2020·Nature·Ka Man YipHolger Stark
Dec 4, 2020·Nature·Vaithish VelazhahanChristopher G Tate
Oct 23, 2020·Nature·Takanori NakaneSjors H W Scheres
Jan 31, 2021·Nature Communications·Zhan YinJudy Hirst
Dec 19, 2020·Molecular Cell·Yong Zi Tan, Bridget Carragher
Feb 27, 2021·Science·Girish R MaliAndrew P Carter
Mar 1, 2021·The Journal of Biological Chemistry·Mikhail A HameediJudy Hirst
Oct 7, 2020·Journal of Structural Biology·Joseph CaesarHans Elmlund
Mar 14, 2021·Nature Communications·Qiuye LiWitold K Surewicz
Mar 19, 2021·Nature·Menghang HuangJijie Chai

❮ Previous
Next ❯

Methods Mentioned

BETA
electron cryo-microscopy
electron-scattering

Software Mentioned

MotionCor
JSPR
RELION

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.