Cited by 13Mosquito-borne diseases and controlEnzyme Structure and FunctionSARS-CoV-2 and COVID-19 Research

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Structural basis of Zika virus NS1 multimerization and human antibody recognition

Open access

Published version of a preprint

Abstract

Zika virus (ZIKV) belongs to the Flavivirus genus of the Flaviviridae family along with the four serotypes of dengue virus (DENV1–4). The recent global outbreaks of contemporary ZIKV strains demonstrated that infection can lead to neurological sequelae in adults and severe abnormalities in newborns that were previously unreported with ancestral strains. As such, there remains an unmet need for efficacious vaccines and antiviral agents against ZIKV. The non-structural protein 1 (NS1) is secreted from the infected cell and is thought to be associated with disease severity besides its proven usefulness for differential diagnoses. However, its physiologically relevant structure and pathogenesis mechanisms remain unclear. Here, we present high-resolution cryoEM structures of ZIKV recombinant secreted NS1 (rsNS1) and its complexes with three human monoclonal antibodies (AA12, EB9, GB5), as well as evidence for ZIKV infection-derived secreted NS1 (isNS1) binding to High Density Lipoprotein (HDL). We show that ZIKV rsNS1 forms tetramers and filamentous repeats of tetramers. We also observed that antibody binding did not disrupt the ZIKV NS1 tetramers as they bound to the wing and connector subdomain of the β-ladder. Our study reveals new insights into NS1 multimerization, highlights the need to distinguish the polymorphic nature of rsNS1 and isNS1, and expands the mechanistic basis of the protection conferred by antibodies targeting NS1.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s44298-024-00024-6

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 58

  1. Ruchusatsawat, K. et al. Long-term circulation of Zika virus in Thailand: an observational study. Lancet Infect. Dis. 19, 439–446 (2019). · DOI
  2. Hill, S. C. et al. Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation. Lancet Infect. Dis. 19, 1138–1147 (2019). · DOI
  3. Scaturro, P., Cortese, M., Chatel-Chaix, L., Fischl, W. & Bartenschlager, R. Dengue virus non-structural protein 1 modulates infectious particle production via interaction with the structural proteins. PLoS Pathog. 11, e1005277 (2015). · DOI
  4. Lindenbach, B. D. & Rice, C. M. Genetic interaction of flavivirus nonstructural proteins NS1 and NS4A as a determinant of replicase function. J. Virol. 73, 4611–4621 (1999). · DOI
  5. Plaszczyca, A. et al. A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle. PLoS Pathog. 15, e1007736 (2019). · DOI
  6. Noisakran, S. et al. Association of dengue virus NS1 protein with lipid rafts. J. Gen. Virol. 89, 2492–2500 (2008). · DOI
  7. Alcon-LePoder, S. et al. Secretion of flaviviral non-structural protein NS1: from diagnosis to pathogenesis. Novartis Found. Symp. 277, 233–247 (2006). · DOI
  8. Xu, X. et al. Contribution of intertwined loop to membrane association revealed by Zika virus full-length NS1 structure. EMBO J. 35, 2170–2178 (2016). · DOI
  9. Puerta-Guardo, H. et al. Flavivirus NS1 triggers tissue-specific vascular endothelial dysfunction reflecting disease tropism. Cell Rep. 26, 1598.e8–1613.e8 (2019). · DOI
  10. Bailey, M. J. et al. Human antibodies targeting Zika virus NS1 provide protection against disease in a mouse model. Nat. Commun. 9, 4560 (2018).
  11. Wessel, A. W. et al. Antibodies targeting epitopes on the cell-surface form of NS1 protect against Zika virus infection during pregnancy. Nat. Commun. 11, 5278 (2020). · DOI
  12. Modhiran, N. et al. A broadly protective antibody that targets the flavivirus NS1 protein. Science 371, 190–194 (2021). · DOI
  13. Biering, S. B. et al. Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction. Science 371, 194–200 (2021). · DOI
  14. Yu, L. et al. Monoclonal antibodies against Zika virus NS1 protein confer protection via Fcγ receptor-dependent and -independent pathways. mBio https://doi.org/10.1128/mBio.03179-20 (2021). · DOI
  15. Chung, K. M. et al. Antibodies against West Nile Virus nonstructural protein NS1 prevent lethal infection through Fc gamma receptor-dependent and -independent mechanisms. J. Virol. 80, 1340–1351 (2006). · DOI
  16. Bailey, M. J. et al. Antibodies elicited by an NS1-based vaccine protect mice against Zika virus. mBio https://doi.org/10.1128/mbio.02861-02818 (2019). · DOI
  17. Glasner, D. R., Puerta-Guardo, H., Beatty, P. R. & Harris, E. The good, the bad, and the shocking: the multiple roles of dengue virus nonstructural protein 1 in protection and pathogenesis. Annu. Rev. Virol. 5, 227–253 (2018). · DOI
  18. Carpio, K. L. & Barrett, A. D. T. Flavivirus NS1 and its potential in vaccine development. Vaccines https://doi.org/10.3390/vaccines9060622 (2021). · DOI
  19. van den Elsen, K., Chew, B. L. A., Ho, J. S. & Luo, D. Flavivirus nonstructural proteins and replication complexes as antiviral drug targets. Curr. Opin Virol. 59, 101305 (2023). · DOI
  20. Akey, D. L. et al. Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system. Science 343, 881–885 (2014). · DOI
  21. Brown, W. C. et al. Extended surface for membrane association in Zika virus NS1 structure. Nat. Struct. Mol. Biol. 23, 865–867 (2016). · DOI
  22. Hertz, T. et al. Antibody epitopes identified in critical regions of dengue virus nonstructural 1 protein in mouse vaccination and natural human infections. J. Immunol. 198, 4025–4035 (2017). · DOI
  23. Bosch, I. et al. Rapid antigen tests for dengue virus serotypes and Zika virus in patient serum. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aan1589 (2017). · DOI
  24. Shu, B. et al. CryoEM structures of the multimeric secreted NS1, a major factor for dengue hemorrhagic fever. Nat. Commun. 13, 6756 (2022).
  25. Flamand, M. et al. Dengue virus type 1 nonstructural glycoprotein NS1 is secreted from mammalian cells as a soluble hexamer in a glycosylation-dependent fashion. J. Virol. 73, 6104–6110 (1999). · DOI
  26. Gutsche, I. et al. Secreted dengue virus nonstructural protein NS1 is an atypical barrel-shaped high-density lipoprotein. Proc. Natl Acad. Sci. USA 108, 8003–8008 (2011). · DOI
  27. Muller, D. A. et al. Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis. J. Gen. Virol. 93, 771–779 (2012). · DOI
  28. Chew, B. L. A. et al. Secreted dengue virus NS1 from infection is predominantly dimeric and in complex with high-density lipoprotein. eLife 12, RP90762 (2023). · DOI
  29. Coelho, D. R. et al. ApoA1 neutralizes proinflammatory effects of dengue virus NS1 protein and modulates viral immune evasion. J. Virol. 95, e0197420 (2021). · DOI
  30. Benfrid, S. et al. Dengue virus NS1 protein conveys pro-inflammatory signals by docking onto high-density lipoproteins. EMBO Rep. 23, e53600 (2022). · DOI
  31. Alcala, A. C. et al. Dengue yirus NS1 uses scavenger receptor B1 as a cell receptor in cultured cells. J. Virol. 96, e0166421 (2022). · DOI
  32. Edeling, M. A., Diamond, M. S. & Fremont, D. H. Structural basis of Flavivirus NS1 assembly and antibody recognition. Proc. Natl Acad. Sci. USA 111, 4285–4290 (2014). · DOI
  33. Han, Y. et al. High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy. Proc. Natl. Acad. Sci. USA 117, 1009–1014 (2020). · DOI
  34. Ereno-Orbea, J. et al. Structural basis of enhanced crystallizability induced by a molecular chaperone for antibody antigen-binding fragments. J. Mol. Biol. 430, 322–336 (2018). · DOI
  35. Bloch, J. S. et al. Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins. Proc. Natl Acad. Sci. USA 118, e2115435118 (2021). · DOI · Paper page
  36. Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020). · DOI
  37. Barad, B. A. et al. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015). · DOI · Paper page
  38. Alcala, A. C. & Ludert, J. E. The dengue virus NS1 protein; new roles in pathogenesis due to similarities with and affinity for the high-density lipoprotein (HDL)? PLoS Pathog. 19, e1011587 (2023). · DOI
  39. Ci, Y. et al. Zika NS1-induced ER remodeling is essential for viral replication. J. Cell Biol. https://doi.org/10.1083/jcb.201903062 (2020). · DOI
  40. Pan, Q. et al. Structural insights into the distinct protective mechanisms of human antibodies targeting ZIKV NS1. Preprint at bioRxiv https://doi.org/10.1101/2023.10.16.562450 (2023). · DOI
  41. Gorman, C. M., Howard, B. H. & Reeves, R. Expression of recombinant plasmids in mammalian cells is enhanced by sodium butyrate. Nucleic Acids Res. 11, 7631–7648 (1983). · DOI
  42. Studier, F. W. In Structural Genomics: General Applications (ed. Chen, Y. W.) 17–32 (Humana Press, 2014). · DOI · Paper page
  43. Pardon, E. et al. A general protocol for the generation of nanobodies for structural biology. Nat. Protoc. 9, 674–693 (2014). · DOI
  44. de la Rosa-Trevín, J. M. et al. Scipion: a software framework toward integration, reproducibility and validation in 3D electron microscopy. J. Struct. Biol. 195, 93–99 (2016). · DOI
  45. de la Rosa-Trevín, J. M. et al. Xmipp 3.0: an improved software suite for image processing in electron microscopy. J. Struct. Biol. 184, 321–328 (2013). · DOI
  46. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife https://doi.org/10.7554/eLife.42166 (2018). · DOI
  47. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
  48. Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019). · DOI
  49. Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019). · DOI
  50. Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021). · DOI
  51. Punjani, A. & Fleet, D. J. 3DFlex: determining structure and motion of flexible proteins from cryo-EM. Nat. Methods 20, 860–870 (2023). · DOI
  52. Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022). · DOI · Paper page
  53. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010). · DOI · Paper page
  54. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019). · DOI · Paper page
  55. Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519–530 (2018). · DOI
  56. Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021). · DOI
  57. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). · DOI
  58. Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. eLife 7, e35383 (2018). · DOI

Metadata

Authors
Chew, B. L. A., Ngoh, A. Q., Phoo, W. W., Weng, M. J. G., Sheng, H. J., Chan, K. W. K., Tan, E. Y. J., Gelbart, T., Xu, C., Tan, G. S., Vasudevan, S. G., & Luo, D.
Affiliations
  • Nanyang Technological University (SG)
  • Duke-NUS Medical School (SG)
  • J. Craig Venter Institute (US)
Corresponding author
Vasudevan, Subhash G.
Venue
npj Viruses
Published
2024-04-25
Volume
2
Issue
1
Pages
14-14
ISSN
2948-1767 (ISSN-L)
OpenAlex
W4395463826
Cited by
13
References
1
Citations by year
2026: 3 · 2025: 3 · 2024: 7
FWCI
5.31
Type
journal article
Language
en
Open access
Locations
  • npj Viruses (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DR-NTU (Nanyang Technological University) (submittedVersion)
Funders
  • National Medical Research Council of Singapore (MOH-OFIRG18may-0006; MOH-OFIRG20nov-0002)
  • Singapore Ministry of Education Academic Research Fund Tier 2 (T2EP30220-0020)
Topics
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mosquito-borne diseases and control
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Keywords
Zika virus, NS1 protein, multimerization, tetramer structure, monoclonal antibodies, antibody binding, high-density lipoprotein, flavivirus, vaccine targets, antiviral agents

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review