2.9 Å Resolution Cryo-EM 3D Reconstruction of Close-Packed Virus Particles

Structure
Zheng LiuWen Jiang

Abstract

Single-particle cryoelectron microscopy typically discards close-packed particle images as unusable data. Here, we report an image processing strategy and case study of obtaining near-atomic resolution 3D reconstructions from close-packed particles. Multiple independent de novo initial models were constructed to determine and cross-validate the particle parameters. The particles with consistent views were further refined including not only Euler angles and center positions but also defocus, astigmatism, beam tilt, and overall and anisotropic magnification. We demonstrated this strategy with a 2.9 Å resolution reconstruction of a 1.67 MDa virus-like particle of a circovirus, PCV2, recorded on 86 photographic films. The map resolution was further validated with a phase-randomization test and local resolution assessment, and the atomic model was validated with MolProbity and EMRinger. Close-packed virus particles were thus shown not only to be useful for high-resolution 3D reconstructions but also to allow data collection at significantly improved throughput for near-atomic resolution reconstructions.

References

Dec 22, 1999·Journal of Structural Biology·S J LudtkeW Chiu
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Jul 25, 2006·Journal of Structural Biology·Guang TangSteven J Ludtke
Sep 12, 2006·Journal of Structural Biology·Thomas D GoddardThomas E Ferrin
Sep 19, 2006·Journal of Structural Biology·Xiaodong YanTimothy S Baker
Dec 21, 2006·Nature Methods·Sjors H W ScheresJose-Maria Carazo
Jan 5, 2007·Annual Review of Biophysics and Biomolecular Structure·Andres E Leschziner, Eva Nogales
Feb 2, 2008·Proceedings of the National Academy of Sciences of the United States of America·Xing ZhangNikolaus Grigorieff
Aug 4, 2009·Virus Research·Tim Finsterbusch, Annette Mankertz
Sep 22, 2009·Current Opinion in Structural Biology·Christian M T Spahn, Pawel A Penczek
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
Feb 22, 2011·Current Opinion in Structural Biology·Nikolaus Grigorieff, Stephen C Harrison
Jun 2, 2011·Journal of Structural Biology·Xing Zhang, Z Hong Zhou
Sep 24, 2011·Journal of Molecular Biology·Richard HendersonPeter B Rosenthal
Feb 14, 2012·Structure·Richard HendersonCatherine L Lawson
Jul 31, 2012·Journal of Structural Biology·Wen JiangZheng Liu
Jul 31, 2012·Nature Methods·Sjors H W Scheres, Shaoxia Chen
Jul 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Matthew L BakerWah Chiu
Nov 6, 2013·Journal of Structural Biology·Rachel S RuskinNikolaus Grigorieff
Mar 29, 2014·Science·Alexey AmuntsV Ramakrishnan
Oct 15, 2014·Proceedings of the National Academy of Sciences of the United States of America·Fei GuoWen Jiang
Feb 15, 2015·Journal of Structural Biology·Vahid AbrishamiJosé María Carazo
Jun 19, 2015·Journal of Structural Biology·Jianhua ZhaoJohn L Rubinstein
Aug 19, 2015·Journal of Structural Biology·Timothy Grant, Nikolaus Grigorieff
Aug 19, 2015·Nature Methods·Benjamin A BaradJames S Fraser

❮ Previous
Next ❯

Citations

Nov 8, 2016·Biophysical Reports·Zheng Liu, Jingqiang Zhang
Oct 30, 2016·Proceedings of the National Academy of Sciences of the United States of America·Zheng LiuJoachim Frank
Nov 2, 2016·Computational and Structural Biotechnology Journal·Slavica Jonić
Oct 28, 2016·Protein Science : a Publication of the Protein Society·Zheng LiuJoachim Frank
Mar 9, 2017·Proceedings of the National Academy of Sciences of the United States of America·Corey F HrycWah Chiu
Mar 17, 2017·Nature Communications·S Saif HasanMichael G Rossmann
Feb 7, 2017·BioMed Research International·Dong Si, Jing He
Dec 8, 2017·Scientific Reports·Marie C StarkR Holland Cheng
Sep 23, 2018·Protein Science : a Publication of the Protein Society·Jimin WangPeter B Moore
Nov 13, 2017·Brazilian Journal of Microbiology : [publication of the Brazilian Society for Microbiology]·Danielle GavaRejane Schaefer
Mar 29, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Todor Kirilov AvramovDong Si
Dec 28, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Eman Alnabati, Daisuke Kihara
May 28, 2020·Bioscience Reports·Mingfang BiXiaobing Mo
Jul 25, 2018·Frontiers in Cellular and Infection Microbiology·Dongliang WangYi Yang
Mar 9, 2018·PloS One·David E TimmCharles Rauch
Sep 9, 2018·Nature Communications·Yong Zi TanDmitry Lyumkis
Jul 19, 2017·Annual Review of Virology·Jason T KaelberWah Chiu
Dec 5, 2020·Viral Immunology·Babu Kanti NathJade K Forwood
Jul 6, 2020·Progress in Biophysics and Molecular Biology·Chen SunWen Jiang
Jun 19, 2021·Journal of Chemical Information and Modeling·Takaharu MoriYuji Sugita
Feb 1, 2020·Journal of Chemical Information and Modeling·Sandhya P TiwariOsamu Miyashita
Feb 27, 2020·Journal of Chemical Information and Modeling·Pilar Cossio
Nov 3, 2021·Physical Chemistry Chemical Physics : PCCP·Elvira TarasovaMakoto Taiji
Nov 28, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Maytha Alshammari, Jing He

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.