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

Abstract

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. Complementarymore » structure-directed mutagenesis identifies critical residues conserved across the filovirus family that could be targeted by broadly effective antivirals.« less

Authors:
 [1];  [2];  [1];  [1];  [2];  [2]; ORCiD logo [3]
  1. The Scripps Research Inst., La Jolla, CA (United States); La Jolla Institute for Immunology, La Jolla, CA (United States)
  2. The Scripps Research Inst., La Jolla, CA (United States)
  3. 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)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
Contributing Org.:
Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
OSTI Identifier:
1559324
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 10; Journal Issue: 4; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Landeras-Bueno, Sara, Oda, Shun-ichiro, Norris, Michael J., Li Salie, Zhe, Guenaga, Javier, Wyatt, Richard T., and Saphire, Erica Ollmann. Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment. United States: N. p., 2019. Web. doi:10.1128/mbio.00734-19.
Landeras-Bueno, Sara, Oda, Shun-ichiro, Norris, Michael J., Li Salie, Zhe, Guenaga, Javier, Wyatt, Richard T., & Saphire, Erica Ollmann. Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment. United States. https://doi.org/10.1128/mbio.00734-19
Landeras-Bueno, Sara, Oda, Shun-ichiro, Norris, Michael J., Li Salie, Zhe, Guenaga, Javier, Wyatt, Richard T., and Saphire, Erica Ollmann. Tue . "Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment". United States. https://doi.org/10.1128/mbio.00734-19. https://www.osti.gov/servlets/purl/1559324.
@article{osti_1559324,
title = {Sudan Ebolavirus VP35-NP Crystal Structure Reveals a Potential Target for Pan-Filovirus Treatment},
author = {Landeras-Bueno, Sara and Oda, Shun-ichiro and Norris, Michael J. and Li Salie, Zhe and Guenaga, Javier and Wyatt, Richard T. and Saphire, Erica Ollmann},
abstractNote = {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.},
doi = {10.1128/mbio.00734-19},
journal = {mBio (Online)},
number = 4,
volume = 10,
place = {United States},
year = {Tue Jul 23 00:00:00 EDT 2019},
month = {Tue Jul 23 00:00:00 EDT 2019}
}

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Works referenced in this record:

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography
journal, February 2012

  • Bharat, T. A. M.; Noda, T.; Riches, J. D.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 11
  • DOI: 10.1073/pnas.1120453109

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Identification and analysis of ebola virus messenger RNA
journal, April 1987


Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers
journal, September 2011

  • Gerritz, S. W.; Cianci, C.; Kim, S.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 37
  • DOI: 10.1073/pnas.1107906108

The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes
journal, March 2013

  • Turrell, Lauren; Lyall, Jon W.; Tiley, Laurence S.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms2589

Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex
journal, July 2015


Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Structure of Nipah virus unassembled nucleoprotein in complex with its viral chaperone
journal, August 2014

  • Yabukarski, Filip; Lawrence, Philip; Tarbouriech, Nicolas
  • Nature Structural & Molecular Biology, Vol. 21, Issue 9
  • DOI: 10.1038/nsmb.2868

The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication
journal, April 2002


Morphology of Marburg Virus NP–RNA
journal, May 2002


P-Protein of Chandipura Virus Is an N-Protein-Specific Chaperone That Acts at the Nucleation Stage
journal, March 2004

  • Majumdar, Amitabha; Bhattacharya, Raja; Basak, Soumen
  • Biochemistry, Vol. 43, Issue 10
  • DOI: 10.1021/bi035793r

Mutual Antagonism between the Ebola Virus VP35 Protein and the RIG-I Activator PACT Determines Infection Outcome
journal, July 2013


Cryo-EM structure of the Ebola virus nucleoprotein–RNA complex at 3.6 Å resolution
journal, October 2018


An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions
journal, April 2015


Influenza A virus nucleoprotein is a major target antigen for cross-reactive anti-influenza A virus cytotoxic T lymphocytes.
journal, March 1985

  • Yewdell, J. W.; Bennink, J. R.; Smith, G. L.
  • Proceedings of the National Academy of Sciences, Vol. 82, Issue 6
  • DOI: 10.1073/pnas.82.6.1785

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

The Ebola virus ribonucleoprotein complex: A novel VP30–L interaction identified
journal, March 2009


Identification of influenza A nucleoprotein body domain residues essential for viral RNA expression expose antiviral target
journal, February 2017


The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses
journal, August 2018


Structure and assembly of the Ebola virus nucleocapsid
journal, November 2017

  • Wan, William; Kolesnikova, Larissa; Clarke, Mairi
  • Nature, Vol. 551, Issue 7680
  • DOI: 10.1038/nature24490

Structure of the Vesicular Stomatitis Virus N0-P Complex
journal, September 2011


Influenza A Virus Nucleoprotein: A Highly Conserved Multi-Functional Viral Protein as a Hot Antiviral Drug Target
journal, July 2017


Influenza virus nucleoprotein: structure, RNA binding, oligomerization and antiviral drug target
journal, December 2013

  • Chenavas, Sylvie; Crépin, Thibaut; Delmas, Bernard
  • Future Microbiology, Vol. 8, Issue 12
  • DOI: 10.2217/fmb.13.128

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Identification of influenza A nucleoprotein as an antiviral target
journal, May 2010

  • Kao, Richard Y.; Yang, Dan; Lau, Lai-Shan
  • Nature Biotechnology, Vol. 28, Issue 6
  • DOI: 10.1038/nbt.1638

Crystal structure of the C-terminal domain of Ebola virus VP30 reveals a role in transcription and nucleocapsid association
journal, January 2007

  • Hartlieb, B.; Muziol, T.; Weissenhorn, W.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 2
  • DOI: 10.1073/pnas.0606730104

Filovirus replication and transcription
journal, March 2007


The RNA synthesis machinery of negative-stranded RNA viruses
journal, May 2015


PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
journal, December 2019


Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021


Overview of the CCP4 suite and current developments.
text, January 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.52322

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Morphology of Marburg Virus NP–RNA
journal, May 2002


Identification and analysis of ebola virus messenger RNA
journal, April 1987


Sequence analysis of the Ebola virus genome: organization, genetic elements, and comparison with the genome of Marburg virus
journal, September 1993


An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions
journal, April 2015


Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex
journal, July 2015


Mutual Antagonism between the Ebola Virus VP35 Protein and the RIG-I Activator PACT Determines Infection Outcome
journal, July 2013


The Ebola virus ribonucleoprotein complex: A novel VP30–L interaction identified
journal, March 2009


P-Protein of Chandipura Virus Is an N-Protein-Specific Chaperone That Acts at the Nucleation Stage
journal, March 2004

  • Majumdar, Amitabha; Bhattacharya, Raja; Basak, Soumen
  • Biochemistry, Vol. 43, Issue 10
  • DOI: 10.1021/bi035793r

Structure and assembly of the Ebola virus nucleocapsid
journal, November 2017

  • Wan, William; Kolesnikova, Larissa; Clarke, Mairi
  • Nature, Vol. 551, Issue 7680
  • DOI: 10.1038/nature24490

Identification of influenza A nucleoprotein as an antiviral target
journal, May 2010

  • Kao, Richard Y.; Yang, Dan; Lau, Lai-Shan
  • Nature Biotechnology, Vol. 28, Issue 6
  • DOI: 10.1038/nbt.1638

The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes
journal, March 2013

  • Turrell, Lauren; Lyall, Jon W.; Tiley, Laurence S.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms2589

Structure of Nipah virus unassembled nucleoprotein in complex with its viral chaperone
journal, August 2014

  • Yabukarski, Filip; Lawrence, Philip; Tarbouriech, Nicolas
  • Nature Structural & Molecular Biology, Vol. 21, Issue 9
  • DOI: 10.1038/nsmb.2868

Cryo-EM structure of the Ebola virus nucleoprotein–RNA complex at 3.6 Å resolution
journal, October 2018


Crystal structure of the C-terminal domain of Ebola virus VP30 reveals a role in transcription and nucleocapsid association
journal, January 2007

  • Hartlieb, B.; Muziol, T.; Weissenhorn, W.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 2
  • DOI: 10.1073/pnas.0606730104

Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers
journal, September 2011

  • Gerritz, S. W.; Cianci, C.; Kim, S.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 37
  • DOI: 10.1073/pnas.1107906108

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography
journal, February 2012

  • Bharat, T. A. M.; Noda, T.; Riches, J. D.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 11
  • DOI: 10.1073/pnas.1120453109

The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication
journal, April 2002


Ebola Virus VP35 Antagonizes PKR Activity through Its C-Terminal Interferon Inhibitory Domain
journal, June 2009

  • Schumann, M.; Gantke, T.; Muhlberger, E.
  • Journal of Virology, Vol. 83, Issue 17
  • DOI: 10.1128/jvi.00523-09

The VP35 Protein of Ebola Virus Inhibits the Antiviral Effect Mediated by Double-Stranded RNA-Dependent Protein Kinase PKR
journal, October 2006


Ebola Virus Protein VP35 Impairs the Function of Interferon Regulatory Factor-Activating Kinases IKK  and TBK-1
journal, January 2009

  • Prins, K. C.; Cardenas, W. B.; Basler, C. F.
  • Journal of Virology, Vol. 83, Issue 7
  • DOI: 10.1128/jvi.01875-08

Ebola Virus VP30-Mediated Transcription Is Regulated by RNA Secondary Structure Formation
journal, September 2002


Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells
journal, November 2014


Structure of the Vesicular Stomatitis Virus N0-P Complex
journal, September 2011


PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Influenza A Virus Nucleoprotein: A Highly Conserved Multi-Functional Viral Protein as a Hot Antiviral Drug Target
journal, July 2017


Filovirus replication and transcription
journal, March 2007


Influenza virus nucleoprotein: structure, RNA binding, oligomerization and antiviral drug target
journal, December 2013

  • Chenavas, Sylvie; Crépin, Thibaut; Delmas, Bernard
  • Future Microbiology, Vol. 8, Issue 12
  • DOI: 10.2217/fmb.13.128