Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment

Landeras-Bueno, Sara; Oda, Shun-ichiro; Norris, Michael J.; Li Salie, Zhe; Guenaga, Javier; Wyatt, Richard T.; Saphire, Erica Ollmann

doi:10.1128/mbio.00734-19

Title: Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment

Journal Article · Tue Jul 23 00:00:00 EDT 2019 · mBio (Online)

DOI:https://doi.org/10.1128/mbio.00734-19· OSTI ID:1559324

Landeras-Bueno, Sara ^[1]; Oda, Shun-ichiro ^[2]; Norris, Michael J. ^[1]; Li Salie, Zhe ^[1]; Guenaga, Javier ^[2]; Wyatt, Richard T. ^[2];

^[3]

The Scripps Research Inst., La Jolla, CA (United States); La Jolla Institute for Immunology, La Jolla, CA (United States)
The Scripps Research Inst., La Jolla, CA (United States)
The Scripps Research Inst., La Jolla, CA (United States); La Jolla Institute for Immunology, La Jolla, CA (United States); Skaggs Institute for Chemical Biology, La Jolla, CA (United States)

The filoviruses are etiological agents of life-threatening hemorrhagic fever with high mortality rate and risk of potential outbreak. Among members of this family, the Ebola (EBOV), Sudan (SUDV), and Marburg (MARV) viruses are considered the most pathogenic for humans. The ebolavirus nucleoprotein (NP) is the most abundant protein in infected cells and is essential for viral transcription and replication; thus, it represents an attractive target for therapeutic intervention. Here, we present the structure of SUDV NP in complex with the amino-terminal portion of the phosphoprotein VP35 at 2.3 Å. This structure captures VP35 chaperoning SUDV NP in a monomeric and RNA-free state. This transient state has been proposed to be key to maintaining a pool of monomeric and RNA-free NPs prior to NP-NP polymerization and encapsidation of the viral RNA genome. This structure also reveals a newly visualized interaction between NP and VP35, a well-defined beta sheet that is not present in previous structures. Affinity binding assays demonstrate that this beta sheet is essential for maintaining the high-affinity interaction between VP35 and a hydrophobic pocket on SUDV NP, and electron microscopy indicates the importance of this binding interaction to the oligomeric state and assembly of NP in human cells. Complementary structure-directed mutagenesis identifies critical residues conserved across the filovirus family that could be targeted by broadly effective antivirals.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Contributing Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

OSTI ID:: 1559324

Journal Information:: mBio (Online), Vol. 10, Issue 4; ISSN 2150-7511

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

Citation Metrics:

Cited by: 6 works

Citation information provided by
Web of Science

References (45)

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography Bharat, T. A. M.; Noda, T.; Riches, J. D. Proceedings of the National Academy of Sciences, Vol. 109, Issue 11 https://doi.org/10.1073/pnas.1120453109	journal	February 2012
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
Identification and analysis of ebola virus messenger RNA Sanchez, Anthony; Kiley, Michael P. Virology, Vol. 157, Issue 2 https://doi.org/10.1016/0042-6822(87)90283-2	journal	April 1987
Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers Gerritz, S. W.; Cianci, C.; Kim, S. Proceedings of the National Academy of Sciences, Vol. 108, Issue 37 https://doi.org/10.1073/pnas.1107906108	journal	September 2011
The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes Turrell, Lauren; Lyall, Jon W.; Tiley, Laurence S. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms2589	journal	March 2013
Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex Kirchdoerfer, Robert N.; Abelson, Dafna M.; Li, Sheng Cell Reports, Vol. 12, Issue 1 https://doi.org/10.1016/j.celrep.2015.06.003	journal	July 2015
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
Structure of Nipah virus unassembled nucleoprotein in complex with its viral chaperone Yabukarski, Filip; Lawrence, Philip; Tarbouriech, Nicolas Nature Structural & Molecular Biology, Vol. 21, Issue 9 https://doi.org/10.1038/nsmb.2868	journal	August 2014
The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication Portela, Agustı́n; Digard, Paul Journal of General Virology, Vol. 83, Issue 4 https://doi.org/10.1099/0022-1317-83-4-723	journal	April 2002
Morphology of Marburg Virus NP–RNA Mavrakis, Manos; Kolesnikova, Larissa; Schoehn, Guy Virology, Vol. 296, Issue 2 https://doi.org/10.1006/viro.2002.1433	journal	May 2002
P-Protein of Chandipura Virus Is an N-Protein-Specific Chaperone That Acts at the Nucleation Stage ^† Majumdar, Amitabha; Bhattacharya, Raja; Basak, Soumen Biochemistry, Vol. 43, Issue 10 https://doi.org/10.1021/bi035793r	journal	March 2004
Mutual Antagonism between the Ebola Virus VP35 Protein and the RIG-I Activator PACT Determines Infection Outcome Luthra, Priya; Ramanan, Parameshwaran; Mire, Chad E. Cell Host & Microbe, Vol. 14, Issue 1 https://doi.org/10.1016/j.chom.2013.06.010	journal	July 2013
Cryo-EM structure of the Ebola virus nucleoprotein–RNA complex at 3.6 Å resolution Sugita, Yukihiko; Matsunami, Hideyuki; Kawaoka, Yoshihiro Nature, Vol. 563, Issue 7729 https://doi.org/10.1038/s41586-018-0630-0	journal	October 2018
An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions Leung, Daisy W.; Borek, Dominika; Luthra, Priya Cell Reports, Vol. 11, Issue 3 https://doi.org/10.1016/j.celrep.2015.03.034	journal	April 2015
Influenza A virus nucleoprotein is a major target antigen for cross-reactive anti-influenza A virus cytotoxic T lymphocytes. Yewdell, J. W.; Bennink, J. R.; Smith, G. L. Proceedings of the National Academy of Sciences, Vol. 82, Issue 6 https://doi.org/10.1073/pnas.82.6.1785	journal	March 1985
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
The Ebola virus ribonucleoprotein complex: A novel VP30–L interaction identified Groseth, A.; Charton, J. E.; Sauerborn, M. Virus Research, Vol. 140, Issue 1-2 https://doi.org/10.1016/j.virusres.2008.10.017	journal	March 2009
Identification of influenza A nucleoprotein body domain residues essential for viral RNA expression expose antiviral target Davis, Alicia M.; Ramirez, Jose; Newcomb, Laura L. Virology Journal, Vol. 14, Issue 1 https://doi.org/10.1186/s12985-017-0694-8	journal	February 2017
The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses Goldstein, Tracey; Anthony, Simon J.; Gbakima, Aiah Nature Microbiology, Vol. 3, Issue 10 https://doi.org/10.1038/s41564-018-0227-2	journal	August 2018
Structure and assembly of the Ebola virus nucleocapsid Wan, William; Kolesnikova, Larissa; Clarke, Mairi Nature, Vol. 551, Issue 7680 https://doi.org/10.1038/nature24490	journal	November 2017
Structure of the Vesicular Stomatitis Virus N0-P Complex Leyrat, Cédric; Yabukarski, Filip; Tarbouriech, Nicolas PLoS Pathogens, Vol. 7, Issue 9 https://doi.org/10.1371/journal.ppat.1002248	journal	September 2011
Influenza A Virus Nucleoprotein: A Highly Conserved Multi-Functional Viral Protein as a Hot Antiviral Drug Target Hu, Yanmei; Sneyd, Hannah; Dekant, Raphael Current Topics in Medicinal Chemistry, Vol. 17, Issue 20 https://doi.org/10.2174/1568026617666170224122508	journal	July 2017
Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide Reveals a Conserved Drug Target for Filovirus Zhu, Tengfei; Song, Hao; Peng, Ruchao Journal of Virology, Vol. 91, Issue 18 https://doi.org/10.1128/JVI.00996-17	journal	June 2017
Influenza virus nucleoprotein: structure, RNA binding, oligomerization and antiviral drug target Chenavas, Sylvie; Crépin, Thibaut; Delmas, Bernard Future Microbiology, Vol. 8, Issue 12 https://doi.org/10.2217/fmb.13.128	journal	December 2013
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Genomic analysis of filoviruses associated with four viral hemorrhagic fever outbreaks in Uganda and the Democratic Republic of the Congo in 2012 Albariño, C. G.; Shoemaker, T.; Khristova, M. L. Virology, Vol. 442, Issue 2 https://doi.org/10.1016/j.virol.2013.04.014	journal	August 2013
The L–VP35 and L–L interaction domains reside in the amino terminus of the Ebola virus L protein and are potential targets for antivirals Trunschke, Martina; Conrad, Dominik; Enterlein, Sven Virology, Vol. 441, Issue 2 https://doi.org/10.1016/j.virol.2013.03.013	journal	July 2013
Identification of influenza A nucleoprotein as an antiviral target Kao, Richard Y.; Yang, Dan; Lau, Lai-Shan Nature Biotechnology, Vol. 28, Issue 6 https://doi.org/10.1038/nbt.1638	journal	May 2010
Crystal structure of the C-terminal domain of Ebola virus VP30 reveals a role in transcription and nucleocapsid association Hartlieb, B.; Muziol, T.; Weissenhorn, W. Proceedings of the National Academy of Sciences, Vol. 104, Issue 2 https://doi.org/10.1073/pnas.0606730104	journal	January 2007
Filovirus replication and transcription Mühlberger, Elke Future Virology, Vol. 2, Issue 2 https://doi.org/10.2217/17460794.2.2.205	journal	March 2007
The RNA synthesis machinery of negative-stranded RNA viruses Ortín, Juan; Martín-Benito, Jaime Virology, Vol. 479-480 https://doi.org/10.1016/j.virol.2015.03.018	journal	May 2015
An N-terminal domain of the Sendai paramyxovirus P protein acts as a chaperone for the NP protein during the nascent chain assembly step of genome replication. Curran, J.; Marq, J. B.; Kolakofsky, D. Journal of virology, Vol. 69, Issue 2 https://doi.org/10.1128/jvi.69.2.849-855.1995	journal	January 1995
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13641-0	journal	December 2019
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
Overview of the CCP4 suite and current developments. Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.52322	text	January 2011
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Sequence analysis of the Ebola virus genome: organization, genetic elements, and comparison with the genome of Marburg virus Sanchez, Anthony; Kiley, Michael P.; Holloway, Brian P. Virus Research, Vol. 29, Issue 3 https://doi.org/10.1016/0168-1702(93)90063-s	journal	September 1993
The Assembly of Ebola Virus Nucleocapsid Requires Virion-Associated Proteins 35 and 24 and Posttranslational Modification of Nucleoprotein Huang, Yue; Xu, Ling; Sun, Yongnian Molecular Cell, Vol. 10, Issue 2 https://doi.org/10.1016/s1097-2765(02)00588-9	journal	August 2002
Ebola Virus VP35 Antagonizes PKR Activity through Its C-Terminal Interferon Inhibitory Domain Schumann, M.; Gantke, T.; Muhlberger, E. Journal of Virology, Vol. 83, Issue 17 https://doi.org/10.1128/jvi.00523-09	journal	June 2009
The VP35 Protein of Ebola Virus Inhibits the Antiviral Effect Mediated by Double-Stranded RNA-Dependent Protein Kinase PKR Feng, Z.; Cerveny, M.; Yan, Z. Journal of Virology, Vol. 81, Issue 1 https://doi.org/10.1128/jvi.01006-06	journal	October 2006
Ebola Virus Protein VP35 Impairs the Function of Interferon Regulatory Factor-Activating Kinases IKK and TBK-1 Prins, K. C.; Cardenas, W. B.; Basler, C. F. Journal of Virology, Vol. 83, Issue 7 https://doi.org/10.1128/jvi.01875-08	journal	January 2009
Three of the Four Nucleocapsid Proteins of Marburg Virus, NP, VP35, and L, Are Sufficient To Mediate Replication and Transcription of Marburg Virus-Specific Monocistronic Minigenomes Mühlberger, Elke; Lötfering, Beate; Klenk, Hans-Dieter Journal of Virology, Vol. 72, Issue 11 https://doi.org/10.1128/jvi.72.11.8756-8764.1998	journal	November 1998
Ebola Virus VP30-Mediated Transcription Is Regulated by RNA Secondary Structure Formation Weik, M.; Modrof, J.; Klenk, H. -D. Journal of Virology, Vol. 76, Issue 17 https://doi.org/10.1128/jvi.76.17.8532-8539.2002	journal	September 2002
Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells Shabman, Reed S.; Jabado, Omar J.; Mire, Chad E. mBio, Vol. 5, Issue 6 https://doi.org/10.1128/mbio.02011-14	journal	November 2014

Cited By (1)

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111 Lin, Aaron E.; Diehl, William E.; Cai, Yingyun Viruses, Vol. 12, Issue 1 https://doi.org/10.3390/v12010105	journal	January 2020

Similar Records

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

Journal Article · Wed Nov 09 00:00:00 EST 2016 · Journal of Virology · OSTI ID:1559324

Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.; +5 more

The Ebola Virus VP30-NP Interaction Is a Regulator of Viral RNA Synthesis

Journal Article · Tue Oct 18 00:00:00 EDT 2016 · PLoS Pathogens · OSTI ID:1559324

Kirchdoerfer, Robert N.; Moyer, Crystal L.; Abelson, Dafna M.; +2 more

Lloviu virus VP24 and VP35 proteins function as innate immune antagonists in human and bat cells

Journal Article · Sun Nov 15 00:00:00 EST 2015 · Virology · OSTI ID:1559324

Feagins, Alicia R.

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment

Citation Formats

References (45)

Cited By (1)

Similar Records

Related Subjects