CoChat
Sign Up
Cited by 4Viral Infectious Diseases and Gene Expression in InsectsAdvanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Structure of AcMNPV nucleocapsid reveals DNA portal organization and packaging apparatus of circular dsDNA baculovirus

Open access
Effantin, Gregory, Kandiah, Eaazhisai, Pelosse, Martin·2025·Nature Communications
DOI 10.1038/s41467-025-60152-2PMC PMC12103608

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Baculoviruses are large DNA viruses found in nature propagating amongst insects and lepidoptera in particular. They have been studied for decades and are nowadays considered as invaluable biotechnology tools used as biopesticides, recombinant expression systems or delivery vehicle for gene therapy. However, little is known about the baculovirus nucleocapsid assembly at a molecular level. Here, we solve the whole structure of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) nucleocapsid by applying cryo-electron microscopy (CryoEM) combined with de novo modelling and Alphafold predictions. Our structure completes prior observations and elucidates the intricate architecture of the apical cap, unravelling the organization of a DNA portal featuring intriguing symmetry mismatches between its core and vertex. The core, closing the capsid at the apex, holds two DNA helices of the viral genome tethered to Ac54 proteins. Different symmetry components at the apical cap and basal structure are constituted of the same building block, made of Ac101/Ac144, proving the versatility of this modular pair. The crown forming the portal vertex displays a C21 symmetry and contains, amongst others, the motor-like protein Ac66. Our findings support the viral portal to be involved in DNA packaging, probably in conjunction with other parts of a larger DNA packaging apparatus.

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/s41467-025-60152-2

Cites

2 of 2 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: 75

  1. Gelaye, Y. & Negash, B. The role of baculoviruses in controlling insect pests: a review. Cogent Food Agriculture 9, 2254139 (2023). · DOI
  2. Inceoglu, A. B. et al. Recombinant baculoviruses for insect control. Pest Manag. Sci. 57, 981–987 (2001). · DOI
  3. Weissmann, F. & Peters, J.-M. Expressing Multi-subunit Complexes Using biGBac. Methods Mol. Biol. 1764, 329–343 (2018). · DOI
  4. Stolt-Bergner, P. et al. Baculovirus-driven protein expression in insect cells: A benchmarking study. J. Struct. Biol. 203, 71–80 (2018). · DOI
  5. Arragain, B., Pelosse, M., Thompson, A. & Cusack, S. Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family. Nat. Commun. 14, 8145 (2023). · DOI
  6. Aulicino, F. et al. Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus. Nucleic Acids Res. 50, 7783–7799 (2022). · DOI
  7. Aulicino, F., Capin, J. & Berger, I. Synthetic virus-derived nanosystems (SVNs) for delivery and precision docking of large multifunctional DNA circuitry in mammalian cells. Pharmaceutics 12, 759 (2020). · DOI
  8. Ono, C., Okamoto, T., Abe, T. & Matsuura, Y. Baculovirus as a tool for gene delivery and gene therapy. Viruses 10, 510 (2018). · DOI
  9. Benning, F. M. C. et al. Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly. Nat. Commun. 15, 250 (2024). · DOI
  10. Jia, X. et al. Architecture of the baculovirus nucleocapsid revealed by cryo-EM. Nat. Commun. 14, 7481 (2023). · DOI
  11. Wang, Q. et al. Budded baculovirus particle structure revisited. J. Invertebr. Pathol. 134, 15–22 (2016). · DOI
  12. Rao, V. B. & Feiss, M. Mechanisms of DNA packaging by large double-stranded DNA viruses. Annu. Rev. Virol. 2, 351–378 (2015). · DOI
  13. Liu, Y.-T., Jih, J., Dai, X., Bi, G.-Q. & Zhou, Z. H. Cryo-EM structures of herpes simplex virus type 1 portal vertex and packaged genome. Nature 570, 257–261 (2019). · DOI
  14. Bauer, D. W., Huffman, J. B., Homa, F. L. & Evilevitch, A. Herpes virus genome, the pressure is on. J. Am. Chem. Soc. 135, 11216–11221 (2013). · DOI
  15. Gong, D. et al. DNA-packing portal and capsid-associated tegument complexes in the tumor herpesvirus KSHV. Cell 178, 1329–1343.e12 (2019). · DOI
  16. Wang, R. et al. Proteomics of the Autographa californica nucleopolyhedrovirus budded virions. J. Virol. 84, 7233–7242 (2010). · DOI
  17. Zhao, S., He, G., Yang, Y. & Liang, C. Nucleocapsid assembly of baculoviruses. Viruses 11, 595 (2019). · DOI
  18. Gao, J. et al. DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models. Structure 32, 1248–1259.e5 (2024). · DOI · Paper page
  19. Meng, E. C. et al. UCSF ChimeraX: Tools for structure building and analysis. Protein Sci. 32, e4792 (2023). · DOI
  20. Ke, J., Wang, J., Deng, R. & Wang, X. Autographa californica multiple nucleopolyhedrovirus ac66 is required for the efficient egress of nucleocapsids from the nucleus, general synthesis of preoccluded virions and occlusion body formation. Virology 374, 421–431 (2008). · DOI
  21. Wu, W. et al. Autographa californica multiple nucleopolyhedrovirus 38K Is a novel nucleocapsid protein that interacts with VP1054, VP39, VP80, and itself. J. Virol. 82, 12356–12364 (2008). · DOI
  22. Olszewski, J. & Miller, L. K. Identification and characterization of a baculovirus structural protein, VP1054, required for nucleocapsid formation. J. Virol. 71, 5040–5050 (1997). · DOI
  23. Guan, Z. et al. The Autographa californica multiple nucleopolyhedrovirus ac54 gene is crucial for localization of the major capsid protein VP39 at the site of nucleocapsid assembly. J. Virol. 90, 4115–4126 (2016). · DOI
  24. Marek, M., Romier, C., Galibert, L., Merten, O.-W. & van Oers, M. M. Baculovirus VP1054 is an acquired cellular PURα, a Nucleic Acid-binding Protein Specific for GGN Repeats. J. Virol. 87, 8465–8480 (2013). · DOI
  25. Holm, L. Using dali for protein structure comparison. Methods Mol. Biol. 2112, 29–42 (2020). · DOI
  26. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792 (2004). · DOI · Paper page
  27. Ac102 Participates in nuclear actin polymerization by modulating BV/ODV-C42 ubiquitination during Autographa californica multiple nucleopolyhedrovirus infection. https://journals.asm.org/doi/epub/10.1128/jvi.00005-18. · DOI
  28. Gandhi, K. M., Ohkawa, T., Welch, M. D. & Volkman, L. E. Nuclear localization of actin requires AC102 in Autographa californica multiple nucleopolyhedrovirus-infected cells. J. Gen. Virol. 93, 1795–1803 (2012). · DOI
  29. Capin, J. et al. An engineered baculoviral protein and DNA co-delivery system for CRISPR-based mammalian genome editing. Nucleic Acids Res. 52, 3450–3468 (2024). · DOI
  30. Sun, M. et al. Ring-stacked capsids of white spot syndrome virus and structural transitions with genome ejection. Sci. Adv. 9, eadd2796 (2023). · DOI
  31. Oppenheimer, D. I. & Volkman, L. E. Evidence for rolling circle replication of Autographa californica M nucleopolyhedrovirus genomic DNA. Arch. Virol. 142, 2107–2113 (1997). · DOI
  32. Vanarsdall, A. L., Okano, K. & Rohrmann, G. F. Characterization of the role of very late expression factor 1 in baculovirus capsid structure and DNA processing. J. Virol. 80, 1724–1733 (2006). · DOI
  33. Braunagel, S. C., Russell, W. K., Rosas-Acosta, G., Russell, D. H. & Summers, M. D. Determination of the protein composition of the occlusion-derived virus of Autographa californica nucleopolyhedrovirus. Proc. Natl Acad. Sci. USA 100, 9797–9802 (2003). · DOI
  34. Jiao, Y., Wang, J., Deng, R., Yu, X. & Wang, X. AcMNPV-miR-3 is a miRNA encoded by Autographa californica nucleopolyhedrovirus and regulates the viral infection by targeting ac101. Virus Res 267, 49–58 (2019). · DOI
  35. Marek, M., van Oers, M. M., Devaraj, F. F., Vlak, J. M. & Merten, O.-W. Engineering of baculovirus vectors for the manufacture of virion-free biopharmaceuticals. Biotechnol. Bioeng. 108, 1056–1067 (2011). · DOI
  36. Houte et al. Protein tyrosine phosphatase-induced hyperactivity is a conserved strategy of a subset of baculoviruses to manipulate lepidopteran host behavior. PLOS ONE 7, e46933 (2012). · DOI
  37. Takagi, T., Taylor, G. S., Kusakabe, T., Charbonneau, H. & Buratowski, S. A protein tyrosine phosphatase-like protein from baculovirus has RNA 5’-triphosphatase and diphosphatase activities. Proc. Natl Acad. Sci. USA 95, 9808–9812 (1998). · DOI
  38. Chen, T. et al. Systematic analysis of 42 Autographa californica multiple nucleopolyhedrovirus genes identifies an additional six genes involved in the production of infectious budded virus. Virol. Sin. 36, 762–773 (2021). · DOI
  39. Hepp, S. E., Borgo, G. M., Ticau, S., Ohkawa, T. & Welch, M. D. Baculovirus AC102 is a nucleocapsid protein that is crucial for nuclear actin polymerization and nucleocapsid morphogenesis. J. Virol. 92, e00111–e00118 (2018). · DOI
  40. Vanarsdall, A. L., Pearson, M. N. & Rohrmann, G. F. Characterization of baculovirus constructs lacking either the Ac 101, Ac 142, or the Ac 144 open reading frame. Virology 367, 187–195 (2007). · DOI
  41. Braunagel, S. C., Guidry, P. A., Rosas-Acosta, G., Engelking, L. & Summers, M. D. Identification of BV/ODV-C42, an autographa californica nucleopolyhedrovirus orf101-encoded structural protein detected in infected-cell complexes with ODV-EC27 and p78/83. J. Virol. 75, 12331–12338 (2001). · DOI
  42. Goley, E. D. et al. Dynamic nuclear actin assembly by Arp2/3 complex and a baculovirus WASP-like protein. Science 314, 464–467 (2006). · DOI
  43. Pearson, M., Bjornson, R., Pearson, G. & Rohrmann, G. The Autographa californica baculovirus genome: evidence for multiple replication origins. Science (New York, N.Y.) 257 (1992). · DOI
  44. Lu, M., Farrell, P. J., Johnson, R. & Iatrou, K. A Baculovirus (Bombyx mori Nuclear Polyhedrosis Virus) Repeat element functions as a powerful constitutive enhancer in transfected insect cells*. J. Biol. Chem. 272, 30724–30728 (1997). · DOI
  45. Perlmutter, J. D. & Hagan, M. F. Mechanisms of virus assembly. Annu Rev. Phys. Chem. 66, 217–239 (2015). · DOI
  46. Ilag, L. L. et al. DNA packaging intermediates of bacteriophage φX174. Structure 3, 353–363 (1995). · DOI
  47. Johnson, S. et al. Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation. Nat. Microbiol. 5, 966–975 (2020). · DOI
  48. Tan, J. et al. Structural basis of assembly and torque transmission of the bacterial flagellar motor. Cell 184, 2665–2679.e19 (2021). · DOI
  49. Li, Z. et al. CryoEM structure of the tegumented capsid of Epstein-Barr virus. Cell Res. 30, 873–884 (2020). · DOI
  50. Li, Y. & Miller, L. K. Expression and localization of a baculovirus protein phosphatase. J. Gen. Virol. 76, 2941–2948 (1995). · DOI
  51. Gross, C. H. & Shuman, S. Characterization of a baculovirus-encoded RNA 5’-triphosphatase. J. Virol. 72, 7057–7063 (1998). · DOI
  52. Wang, J. et al. The conserved domain database in 2023. Nucleic Acids Res. 51, D384–D388 (2023). · DOI · Paper page
  53. Yang, Y. et al. Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation. Protein Cell 11, 339–351 (2020). · DOI
  54. Pajak, J. et al. Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor. Nucleic Acids Res. 49, 6474–6488 (2021). · DOI
  55. Hilbert, B. J. et al. Structure and mechanism of the ATPase that powers viral genome packaging. Proc. Natl Acad. Sci. 112, E3792–E3799 (2015). · DOI
  56. Pajak, J., Prokhorov, N. S., Jardine, P. J. & Morais, M. C. The mechano-chemistry of a viral genome packaging motor. Curr. Opin. Struct. Biol. 89, 102945 (2024). · DOI
  57. Woodson, M. et al. A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. Sci. Adv. 7, eabc1955 (2021). · DOI
  58. Fitzgerald, D. J. et al. Protein complex expression by using multigene baculoviral vectors. Nat. Methods 3, 1021–1032 (2006). · DOI · Paper page
  59. Berger, I., Fitzgerald, D. J. & Richmond, T. J. Baculovirus expression system for heterologous multiprotein complexes. Nat. Biotechnol. 22, 1583–1587 (2004). · DOI
  60. Kandiah, E. et al. CM01: a facility for cryo-electron microscopy at the European Synchrotron. Acta Crystallogr D: Struct. Biol. 75, 528–535 (2019). · DOI
  61. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). · DOI
  62. Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem. J. 478, 4169–4185 (2021). · DOI
  63. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016). · DOI
  64. Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007). · DOI
  65. Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019). · DOI
  66. Pintilie, G. D., Zhang, J., Goddard, T. D., Chiu, W. & Gossard, D. C. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 170, 427–438 (2010). · DOI
  67. Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). · DOI
  68. Nakane, T. & Scheres, S. H. W. Multi-body refinement of cryo-em images in RELION. Methods Mol. Biol. 2215, 145–160 (2021). · DOI
  69. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997). · DOI · Paper page
  70. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990). · DOI · Paper page
  71. Chojnowski, G. et al. findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCrJ 9, 86–97 (2022). · DOI
  72. Wang, R. Y.-R. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. Elife 5, e17219 (2016). · DOI · Paper page
  73. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D: Biol. Crystallogr 66, 213–221 (2010). · DOI · Paper page
  74. 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
  75. Williams, C. J. et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018). · DOI · Paper page

Metadata

Authors
Effantin, G., Kandiah, E., & Pelosse, M.
Affiliations
  • European Synchrotron Radiation Facility (FR)
  • European Molecular Biology Laboratory (FR)
Corresponding author
  • Kandiah, Eaazhisai
  • Pelosse, Martin
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-05-24
Volume
16
Issue
1
Pages
4844-4844
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-60152-2
PMC
PMC12103608
OpenAlex
W4410707185
Cited by
4
References
2
Citations by year
2025: 4
FWCI
1.19
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
European Synchrotron Radiation Facility
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
Autographa californica nuclear polyhedrosis virus, capsid structure, apical cap, symmetry mismatch
MeSH terms
Animals, Capsid, DNA, Circular, DNA, Viral, Models, Molecular, Genome, Viral, Nucleopolyhedroviruses, Spodoptera, Virus Assembly, Nucleocapsid, Cryoelectron Microscopy, Capsid Proteins, Sf9 Cells

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