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Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome [article]

Kaiming Zhang, Ivan N. Zheludev, Rachel J. Hagey, Marie Teng-Pei Wu, Raphael Haslecker, Yixuan J. Hou, Rachael Kretsch, Grigore D. Pintilie, Ramya Rangan, Wipapat Kladwang, Shanshan Li, Edward A. Pham (+7 others)
2020 biorxiv/medrxiv  
To understand current limitations, we applied cryogenic electron microscopy (cryo-EM) and the Ribosolve pipeline to determine a three-dimensional structure of the SARS-CoV-2 FSE, validated through an RNA  ...  The tertiary structure model, defined to an estimated accuracy of 5.9 Å, presents a topologically complex fold in which the 5′ end threads through a ring formed inside a three-stem pseudoknot.  ...  Fig. 2 . 2 Single-particle cryo-EM analysis and model building of the FSE. a. Reference-free 2D class averages. b. Gold standard FSC plots calculated in Relion. c.  ... 
doi:10.1101/2020.07.18.209270 pmid:32743589 pmcid:PMC7386510 fatcat:7duceijrfzemznbh3whm4dak4u

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

George Ueda, Aleksandar Antanasijevic, Jorge A Fallas, William Sheffler, Jeffrey Copps, Daniel Ellis, Geoffrey B Hutchinson, Adam Moyer, Anila Yasmeen, Yaroslav Tsybovsky, Young-Jun Park, Matthew J Bick (+13 others)
2020 eLife  
Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted  ...  To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers  ...  We thank Kathryn Burnett and Greg Hura for SAXS data collection through the SIBYLS mail-in SAXS program.  ... 
doi:10.7554/elife.57659 pmid:32748788 fatcat:oz7vy3ewd5hnxn3lw3c5mnetge

Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens [article]

George Ueda, Aleksandar Antanasijevic, Jorge A Fallas, William Sheffler, Jeffrey Copps, Daniel Ellis, Geoffrey Hutchinson, Adam Moyer, Anila Yasmeen, Yaroslav Tsybovsky, Young-Jun Park, Matthew J Bick (+13 others)
2020 biorxiv/medrxiv   pre-print
in the predicted geometries.  ...  The adaptive immune system is highly sensitive to arrayed antigens, and multivalent display of viral glycoproteins on symmetric scaffolds has been found to substantially increase the elicitation of antigen-specific  ...  We thank Kathryn Burnett and Greg Hura for SAXS data collection through the SIBYLS mail-in SAXS program.  ... 
doi:10.1101/2020.01.29.923862 fatcat:wlr4h7qn6rcjjhsc4tfukiwuou

Exploring applications of crowdsourcing to cryo-EM

Jacob Bruggemann, Gabriel C. Lander, Andrew I. Su
2018 Journal of Structural Biology  
We show the possibilities and limitations of crowdsourcing particle selection tasks, and explore further options for crowdsourcing cryo-EM data processing.  ...  Extraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets.  ...  Scheres, Relion: Implementation of a bayesian approach to cryo-em structure determination, 300 Journal of Structural Biology 180 (3) (2012) 519 -530. doi:https://doi.org/10.1016/j.jsb.2012. 301 09.006.302URL  ... 
doi:10.1016/j.jsb.2018.02.006 pmid:29486249 pmcid:PMC6086358 fatcat:q42mxwfqkzcx5hiqvcqv2rln7y

Structures of human dual oxidase 1 complex in low-calcium and high-calcium states

Jing-Xiang Wu, Rui Liu, Kangcheng Song, Lei Chen
2021 Nature Communications  
Here, we report the cryo-EM structures of human DUOX1-DUOXA1 complex in both high-calcium and low-calcium states.  ...  These structures reveal the DUOX1 complex is a symmetric 2:2 hetero-tetramer stabilized by extensive inter-subunit interactions.  ...  The cryo-EM map of DUOX1-DUOXA1 in the highcalcium and low-calcium states have been deposited in the EMDB under ID code EMD-30556 and EMD-30555.  ... 
doi:10.1038/s41467-020-20466-9 pmid:33420071 fatcat:xit4ust3dvc3pdwlipt35p5kpq

Structure and mechanism of human dual oxidase 1 complex [article]

Jing-Xiang Wu, Rui Liu, Kangcheng Song, Lei Chen
2020 bioRxiv   pre-print
Here, we report the cryo-EM structures of human DUOX1-DUOXA1 complex in both high-calcium and low-calcium states.  ...  In the presence of calcium ions, intracellular EF-hand modules enhance the catalytic activity of DUOX by stabilizing the dehydrogenase domain in a position that is optimal for electron transfer.  ...  Acknowledgement We thank Yunlu Kang, Wenjun Guo, Yange Niu, Dian Ding, Mengmeng Wang, Miao Wei and Xiao He for illustration. We thank Miao Wei for making the rat FSHβ secretion signal-guided  ... 
doi:10.1101/2020.09.23.309245 fatcat:gxwq6wb75fgbplu5fsyfyrqfmi

Exploring Applications of Crowdsourcing to Cryo-EM [article]

Jacob Bruggemann, Gabriel C Lander, Andrew I Su
2017 bioRxiv   pre-print
We show the possibilities and limitations of crowdsourcing particle selection tasks, and explore further options for crowdsourcing cryo-EM data processing.  ...  Extraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets.  ...  Introduction 1 In the past several years cryo-electron microscopy (cryo-EM) has become a powerful tool for elucidating 2 the structures of macromolecular complexes to near-atomic resolution, and has  ... 
doi:10.1101/220145 fatcat:gv655z4mhfcjvgbbtgautdqcqq

High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams

Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen
2021 Communications Biology  
Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM).  ...  This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.  ...  Acknowledgements We thank Keisuke Kawakami for the critical reading of the manuscript.  ... 
doi:10.1038/s42003-021-01919-3 pmid:33753866 fatcat:54ukryybava3hhdeadoqxjkuny

Three epitope-distinct human antibodies from RenMab mice neutralize SARS-CoV-2 and cooperatively minimize the escape of mutants

Jianhui Nie, Jingshu Xie, Shuo Liu, Jiajing Wu, Chuan Liu, Jianhui Li, Yacui Liu, Meiyu Wang, Huizhen Zhao, Yabo Zhang, Jiawei Yao, Lei Chen (+5 others)
2021 Cell Discovery  
We determined the involved residues of the epitope of three representative antibodies by cryo-electron microscopy (Cryo-EM) studies.  ...  Our study provides a sound basis for the rational design of fully human antibody cocktails against SARS-CoV-2 and pre-emergent coronaviral threats.  ...  Further, we performed cryo-electron microscopy (Cryo-EM) structure studies of the spike-Fab complex of three representative antibodies.  ... 
doi:10.1038/s41421-021-00292-z fatcat:zmtjmwwfh5dbdcbfspy3pwqhjm

Identification of changing ribosome protein compositions using cryo-EM and mass spectrometry [article]

Joachim Frank
2018 bioRxiv   pre-print
Cryo-EM shows a fraction (17%) of the ribosome population in yeast growing in glucose lack the ribosomal proteins RPL10 (ul16) and RPS1A/B (eS1).  ...  We applied both cryo-EM and mass spectrometry to identify such changes in S. cerevisiae 80S ribosomes.  ...  Hierarchical classification was performed using the RELION program (Scheres, 2012) , in conjunction with a quantitative analysis of convergence (Chen et al., 2014) .  ... 
doi:10.1101/271833 fatcat:pri6kkjk7ze5xns6rn62e7lgky

Combating the SARS-CoV-2 Omicron variant with non-Omicron neutralizing antibodies [article]

Yingdan Wang, Xiang Zhang, Jiangyan Liu, Yanqun Wang, Wuqiang Zhan, Mei Liu, Meng Zhang, Qimin Wang, Qianying Liu, Tong-Yu Zhu, Yumei Wen, Zhenguo Chen (+4 others)
2022 bioRxiv   pre-print
A cryo-electron microscopy (cryo-EM) structure study of the representative bispecific antibody FD01 in complex with the Omicron spike (S) revealed 5 distinct trimers and one unique bi-trimer conformation  ...  The structure and mapping analyses of 34 Omicron S variant single mutants elucidated that two scFvs of the bispecific antibody synergistically induced the RBD-down conformation into 3-RBD-up conformation  ...  ACKNOWLEDGMENTS AUTHOR CONTRIBUTIONS JH, LS, and FW conceived and designed the experiments. JH, ML, and FW  ... 
doi:10.1101/2022.01.30.478305 fatcat:6scxxmhkfzb5lcekiwqpqbuxva

Two-stage dimension reduction for noisy high-dimensional images and application to Cryogenic Electron Microscopy [article]

Szu-Chi Chung, Shao-Hsuan Wang, Po-Yao Niu, Su-Yun Huang, Wei-Hau Chang, I-Ping Tu
2020 arXiv   pre-print
The first stage treats the image as a matrix, which is a tensor of order 2, and uses multilinear principal component analysis (MPCA) for matrix rank reduction and image denoising.  ...  Applications to cryo-EM (cryogenic electronic microscopy), which has revolutionized structural biology, organic and medical chemistry, cellular and molecular physiology in the past decade, are also provided  ...  Acknowledgement This work is supported by Academia Sinica:AS-GCS-108-08 and MOST:106-2118-M-001-001 -MY2.  ... 
arXiv:1911.09816v3 fatcat:vuyycucsdvhhvkb2xvwcdjkl2y

The Architecture of Talin1 Reveals an Autoinhibition Mechanism

Dirk Dedden, Stephanie Schumacher, Charlotte F. Kelley, Martin Zacharias, Christian Biertümpfel, Reinhard Fässler, Naoko Mizuno
2019 Cell  
To understand how talin function is regulated, we determined a cryoelectron microscopy (cryo-EM) structure of full-length talin1 revealing a two-way mode of autoinhibition.  ...  In turn, the rod domains R9 and R12 shield access of the FERM domain to integrin and the phospholipid PIP2 at the membrane.  ...  ACKNOWLEDGEMENTS We thank Carsten Grashoff and Giovanni Cardone for assistance at various stages of the project, Elena Conti, Wolfgang Baumeister, and the biochemistry-and cryo-EM core facilities for resources  ... 
doi:10.1016/j.cell.2019.08.034 pmid:31539492 pmcid:PMC6856716 fatcat:muyiozlxhrdexhv7aksjnmayda

Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle

Philip J. M. Brouwer, Aleksandar Antanasijevic, Zachary Berndsen, Anila Yasmeen, Brooke Fiala, Tom P. L. Bijl, Ilja Bontjer, Jacob B. Bale, William Sheffler, Joel D. Allen, Anna Schorcht, Judith A. Burger (+19 others)
2019 Nature Communications  
However, NAb responses are relatively weak and narrow in specificity. Displaying antigens in a multivalent fashion on nanoparticles (NPs) is an established strategy to increase their immunogenicity.  ...  Their ability to enhance and shape the immunogenicity of SOSIP trimers make these NPs a promising immunogen platform.  ...  and David Nemazee for kindly sharing  ... 
doi:10.1038/s41467-019-12080-1 pmid:31537780 pmcid:PMC6753213 fatcat:w23y5vqkdvbmvmzmtqqu2um7hi