Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Li, Yunfeng; Pustovalova, Yulia; Shi, Wuxian; Gorbatyuk, Oksana; Sreeramulu, Sridhar; Schwalbe, Harald; Hoch, Jeffrey C.; Hao, Bing

doi:10.1038/s41598-023-30045-9

Title: Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Journal Article · Sat Feb 18 00:00:00 EST 2023 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-023-30045-9· OSTI ID:1957694

Li, Yunfeng; Pustovalova, Yulia; Shi, Wuxian; Gorbatyuk, Oksana; Sreeramulu, Sridhar; Schwalbe, Harald; Hoch, Jeffrey C.; Hao, Bing

Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

View Journal Article

Cite

Export

Save

Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH), National Institute of General Medical Sciences (NIGMS); German Research foundation (DFG); National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0012704; CGC902; GM123249; GM135592; P41GM111135; RAPID 2030601; P30GM133893; AC02-76SF00515; P30GM133894

OSTI ID:: 1957694

Alternate ID(s):: OSTI ID: 1984440

Report Number(s):: BNL-224370-2023-JAAM; 2890; PII: 30045

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Vol. 13 Journal Issue: 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (57)

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia Zaki, Ali M.; van Boheemen, Sander; Bestebroer, Theo M. New England Journal of Medicine, Vol. 367, Issue 19 https://doi.org/10.1056/NEJMoa1211721	journal	November 2012
Proteomics Analysis Unravels the Functional Repertoire of Coronavirus Nonstructural Protein 3 Neuman, Benjamin W.; Joseph, Jeremiah S.; Saikatendu, Kumar S. Journal of Virology, Vol. 82, Issue 11 https://doi.org/10.1128/JVI.02631-07	journal	March 2008
Membranous Replication Factories Induced by Plus-Strand RNA Viruses Romero-Brey, Inés; Bartenschlager, Ralf Viruses, Vol. 6, Issue 7 https://doi.org/10.3390/v6072826	journal	July 2014
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
On the origin and evolution of SARS-CoV-2 Singh, Devika; Yi, Soojin V. Experimental & Molecular Medicine, Vol. 53, Issue 4 https://doi.org/10.1038/s12276-021-00604-z	journal	April 2021
Automated data collection for macromolecular crystallography Winter, Graeme; McAuley, Katherine E. Methods, Vol. 55, Issue 1 https://doi.org/10.1016/j.ymeth.2011.06.010	journal	September 2011
Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein Lei, Jian; Kusov, Yuri; Hilgenfeld, Rolf Antiviral Research, Vol. 149 https://doi.org/10.1016/j.antiviral.2017.11.001	journal	January 2018
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3330	journal	November 2017
The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein Imbert, Isabelle; Snijder, Eric J.; Dimitrova, Maria Virus Research, Vol. 133, Issue 2 https://doi.org/10.1016/j.virusres.2007.11.017	journal	May 2008
Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications Altincekic, Nadide; Korn, Sophie Marianne; Qureshi, Nusrat Shahin Frontiers in Molecular Biosciences, Vol. 8 https://doi.org/10.3389/fmolb.2021.653148	journal	May 2021
Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus nsp3-4 Polyprotein Induce the Formation of Double-Membrane Vesicles That Mimic Those Associated with Coronaviral RNA Replication Oudshoorn, Diede; Rijs, Kevin; Limpens, Ronald W. A. L. mBio, Vol. 8, Issue 6 https://doi.org/10.1128/mBio.01658-17	journal	December 2017
A new coronavirus associated with human respiratory disease in China Wu, Fan; Zhao, Su; Yu, Bin Nature, Vol. 579, Issue 7798 https://doi.org/10.1038/s41586-020-2008-3	journal	February 2020
Evolutionary Relationships and Structural Mechanisms of aaa+ Proteins Erzberger, Jan P.; Berger, James M. Annual Review of Biophysics and Biomolecular Structure, Vol. 35, Issue 1 https://doi.org/10.1146/annurev.biophys.35.040405.101933	journal	June 2006
Membrane lipids: where they are and how they behave van Meer, Gerrit; Voelker, Dennis R.; Feigenson, Gerald W. Nature Reviews Molecular Cell Biology, Vol. 9, Issue 2 https://doi.org/10.1038/nrm2330	journal	February 2008
A Novel Coronavirus Associated with Severe Acute Respiratory Syndrome Ksiazek, Thomas G.; Erdman, Dean; Goldsmith, Cynthia S. New England Journal of Medicine, Vol. 348, Issue 20, p. 1953-1966 https://doi.org/10.1056/NEJMoa030781	journal	May 2003
A molecular pore spans the double membrane of the coronavirus replication organelle Wolff, Georg; Limpens, Ronald W. A. L.; Zevenhoven-Dobbe, Jessika C. Science, Vol. 369, Issue 6509 https://doi.org/10.1126/science.abd3629	journal	August 2020
Evolution of the SARS‐CoV ‐2 proteome in three dimensions (3D) during the first 6 months of the COVID ‐19 pandemic Lubin, Joseph H.; Zardecki, Christine; Dolan, Elliott M. Proteins: Structure, Function, and Bioinformatics, Vol. 90, Issue 5 https://doi.org/10.1002/prot.26250	journal	October 2021
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy J. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6 https://doi.org/10.1107/S0907444909012098	journal	May 2009
Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles Neuman, Benjamin W. Antiviral Research, Vol. 135 https://doi.org/10.1016/j.antiviral.2016.10.005	journal	November 2016
NMR quality control of fragment libraries for screening Sreeramulu, Sridhar; Richter, Christian; Kuehn, Till Journal of Biomolecular NMR, Vol. 74, Issue 10-11 https://doi.org/10.1007/s10858-020-00327-9	journal	June 2020
Using Dali for Protein Structure Comparison Holm, Liisa Methods in Molecular Biology https://doi.org/10.1007/978-1-0716-0270-6_3	book	January 2020
Atomic Structures of the Human Immunophilin FKBP-12 Complexes with FK506 and Rapamycin Van Duyne, Gregory D.; Standaert, Robert F.; Karplus, P. Andrew Journal of Molecular Biology, Vol. 229, Issue 1 https://doi.org/10.1006/jmbi.1993.1012	journal	January 1993
Identification of a Novel Coronavirus in Patients with Severe Acute Respiratory Syndrome Drosten, Christian; Günther, Stephan; Preiser, Wolfgang New England Journal of Medicine, Vol. 348, Issue 20 https://doi.org/10.1056/NEJMoa030747	journal	May 2003
Mobility and Interactions of Coronavirus Nonstructural Protein 4 Hagemeijer, Marne C.; Ulasli, Mustafa; Vonk, Annelotte M. Journal of Virology, Vol. 85, Issue 9 https://doi.org/10.1128/JVI.00042-11	journal	May 2011
Severe Acute Respiratory Syndrome Coronavirus Nonstructural Proteins 3, 4, and 6 Induce Double-Membrane Vesicles Angelini, Megan M.; Akhlaghpour, Marzieh; Neuman, Benjamin W. mBio, Vol. 4, Issue 4 https://doi.org/10.1128/mBio.00524-13	journal	August 2013
SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum Knoops, Kèvin; Kikkert, Marjolein; Worm, Sjoerd H. E. van den PLoS Biology, Vol. 6, Issue 9 https://doi.org/10.1371/journal.pbio.0060226	journal	September 2008
A pneumonia outbreak associated with a new coronavirus of probable bat origin Zhou, Peng; Yang, Xing-Lou; Wang, Xian-Guang Nature, Vol. 579, Issue 7798 https://doi.org/10.1038/s41586-020-2012-7	journal	February 2020
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins Kozakov, Dima; Grove, Laurie E.; Hall, David R. Nature Protocols, Vol. 10, Issue 5 https://doi.org/10.1038/nprot.2015.043	journal	April 2015
Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme Wan, Futang; Wang, Qianmin; Tan, Jing Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10496-3	journal	June 2019
Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci Briliūtė, Justina; Urbanowicz, Paulina A.; Luis, Ana S. Nature Microbiology, Vol. 4, Issue 9 https://doi.org/10.1038/s41564-019-0466-x	journal	June 2019
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks Shen, Yang; Bax, Ad Journal of Biomolecular NMR, Vol. 56, Issue 3 https://doi.org/10.1007/s10858-013-9741-y	journal	June 2013
Membrane rearrangements mediated by coronavirus nonstructural proteins 3 and 4 Hagemeijer, Marne C.; Monastyrska, Iryna; Griffith, Janice Virology, Vol. 458-459 https://doi.org/10.1016/j.virol.2014.04.027	journal	June 2014
Origin and evolution of pathogenic coronaviruses Cui, Jie; Li, Fang; Shi, Zheng-Li Nature Reviews Microbiology, Vol. 17, Issue 3 https://doi.org/10.1038/s41579-018-0118-9	journal	December 2018
The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins Jaroszewski, Lukasz; Iyer, Mallika; Alisoltani, Arghavan PLOS Computational Biology, Vol. 17, Issue 7 https://doi.org/10.1371/journal.pcbi.1009147	journal	July 2021
Structural classification of zinc fingers: SURVEY AND SUMMARY Krishna, S. S. Nucleic Acids Research, Vol. 31, Issue 2 https://doi.org/10.1093/nar/gkg161	journal	January 2003
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic Boni, Maciej F.; Lemey, Philippe; Jiang, Xiaowei Nature Microbiology, Vol. 5, Issue 11 https://doi.org/10.1038/s41564-020-0771-4	journal	July 2020
NMRbox: A Resource for Biomolecular NMR Computation Maciejewski, Mark W.; Schuyler, Adam D.; Gryk, Michael R. Biophysical Journal, Vol. 112, Issue 8 https://doi.org/10.1016/j.bpj.2017.03.011	journal	April 2017
Coronavirus infection induces progressive restructuring of the endoplasmic reticulum involving the formation and degradation of double membrane vesicles Mihelc, Elaine M.; Baker, Susan C.; Lanman, Jason K. Virology, Vol. 556 https://doi.org/10.1016/j.virol.2020.12.007	journal	April 2021
Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors Yanamala, Naveena; Tirupula, Kalyan C.; Klein-Seetharaman, Judith BMC Bioinformatics, Vol. 9, Issue S1 https://doi.org/10.1186/1471-2105-9-S1-S16	journal	February 2008
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs Almasy, Katherine M.; Davies, Jonathan P.; Plate, Lars Molecular & Cellular Proteomics, Vol. 20 https://doi.org/10.1016/j.mcpro.2021.100120	journal	January 2021
Functions of Anionic Lipids in Plants Noack, Lise C.; Jaillais, Yvon Annual Review of Plant Biology, Vol. 71, Issue 1 https://doi.org/10.1146/annurev-arplant-081519-035910	journal	April 2020
Introducing Membrane Charge and Membrane Potential to T Cell Signaling Ma, Yuanqing; Poole, Kate; Goyette, Jesse Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.01513	journal	November 2017
Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite Jurrus, Elizabeth; Engel, Dave; Star, Keith Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3280	journal	October 2017
Structural insights into SARS-CoV-2 proteins Arya, Rimanshee; Kumari, Shweta; Pandey, Bharati Journal of Molecular Biology, Vol. 433, Issue 2 https://doi.org/10.1016/j.jmb.2020.11.024	journal	January 2021
Coronavirus biology and replication: implications for SARS-CoV-2 V’kovski, Philip; Kratzel, Annika; Steiner, Silvio Nature Reviews Microbiology, Vol. 19, Issue 3 https://doi.org/10.1038/s41579-020-00468-6	journal	October 2020
Backbone and Ile, Leu, Val methyl group resonance assignment of CoV-Y domain of SARS-CoV-2 non-structural protein 3 Pustovalova, Yulia; Gorbatyuk, Oksana; Li, Yunfeng Biomolecular NMR Assignments, Vol. 16, Issue 1 https://doi.org/10.1007/s12104-021-10059-y	journal	November 2021
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
A Novel Coronavirus from Patients with Pneumonia in China, 2019 Zhu, Na; Zhang, Dingyu; Wang, Wenling New England Journal of Medicine, Vol. 382, Issue 8 https://doi.org/10.1056/NEJMoa2001017	journal	February 2020
Exploiting Connections for Viral Replication Wong, Louise H.; Edgar, James R.; Martello, Andrea Frontiers in Cell and Developmental Biology, Vol. 9 https://doi.org/10.3389/fcell.2021.640456	journal	March 2021
Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be Mariano, Giuseppina; Farthing, Rebecca J.; Lale-Farjat, Shamar L. M. Frontiers in Molecular Biosciences, Vol. 7 https://doi.org/10.3389/fmolb.2020.605236	journal	December 2020
Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis Chen, Zhen; Suzuki, Hiroshi; Kobayashi, Yuki Cell, Vol. 175, Issue 3 https://doi.org/10.1016/j.cell.2018.09.015	journal	October 2018
A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis Snijder, Eric J.; Limpens, Ronald W. A. L.; de Wilde, Adriaan H. PLOS Biology, Vol. 18, Issue 6 https://doi.org/10.1371/journal.pbio.3000715	journal	June 2020
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Genotype and phenotype of COVID-19: Their roles in pathogenesis Mousavizadeh, Leila; Ghasemi, Sorayya Journal of Microbiology, Immunology and Infection, Vol. 54, Issue 2 https://doi.org/10.1016/j.jmii.2020.03.022	journal	April 2021

Similar Records

Structure of the C-terminal domain of nsp4 from feline coronavirus

Journal Article · Sat Aug 01 00:00:00 EDT 2009 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:1957694

Manolaridis, Ioannis; Wojdyla, Justyna A.; Panjikar, Santosh; +5 more

Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis

Journal Article · Wed Nov 15 00:00:00 EST 2017 · mSphere · OSTI ID:1957694

Menachery, Vineet D.; Gralinski, Lisa E.; Mitchell, Hugh D.; +12 more

The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase

Journal Article · Wed Jan 13 00:00:00 EST 2021 · Journal of Virology · OSTI ID:1957694

Alhammad, Yousef M. O.; Kashipathy, Maithri M.; Roy, Anuradha; +11 more

Related Subjects

36 MATERIALS SCIENCE
Biochemistry
Biophysics
Diseases
Microbiology
Structural biology

Title: Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Citation Formats

References (57)

Similar Records

Related Subjects