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- PDB-8vwh: Structure of the baculovirus major nucleocapsid protein VP39 (loc... -

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Basic information

Entry
Database: PDB / ID: 8vwh
TitleStructure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / Capsid / helical assembly
Function / homologyBaculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / host cell nuclear matrix / virion component / viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesAutographa californica multiple nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsJohnstone, B.A. / Hardy, J.M. / Ha, J.H. / Venugopal, H. / Coulibaly, F.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103388 Australia
National Health and Medical Research Council (NHMRC, Australia)2008096 Australia
CitationJournal: Sci Adv / Year: 2024
Title: The nucleocapsid architecture and structural atlas of the prototype baculovirus define the hallmarks of a new viral realm.
Authors: Bronte A Johnstone / Joshua M Hardy / Jungmin Ha / Anamarija Butkovic / Paulina Koszalka / Cathy Accurso / Hariprasad Venugopal / Alex de Marco / Mart Krupovic / Fasséli Coulibaly /
Abstract: Baculovirus is the most studied insect virus owing to a broad ecological distribution and ease of engineering for biotechnological applications. However, its structure and evolutionary place in the ...Baculovirus is the most studied insect virus owing to a broad ecological distribution and ease of engineering for biotechnological applications. However, its structure and evolutionary place in the virosphere remain enigmatic. Using cryo-electron microscopy, we show that the nucleocapsid forms a covalently cross-linked helical tube protecting a highly compacted 134-kilobase pair DNA genome. The ends of the tube are sealed by the base and cap substructures, which share a 126-subunit hub but differ in components that promote actin tail-mediated propulsion and nuclear entry of the nucleocapsid, respectively. Unexpectedly, sensitive searches for hidden evolutionary links show that the morphogenetic machinery and conserved oral infectivity factors originated within the lineage of baculo-like viruses (class ). The unique viral architecture and structural atlas of hallmark proteins firmly place these viruses into a separate new realm, the highest taxonomy rank, and provide a structural framework to expand their use as sustainable bioinsecticides and biomedical tools.
History
DepositionFeb 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2May 21, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
C: Major capsid protein
E: Major capsid protein
G: Major capsid protein
I: Major capsid protein
K: Major capsid protein
M: Major capsid protein
O: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,38715
Polymers311,9298
Non-polymers4587
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
2
A: Major capsid protein
C: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1134
Polymers77,9822
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major capsid protein


Mass: 38991.109 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: P39, VP39, ORF89 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17499
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Autographa californica multiple nucleopolyhedrovirus / Type: VIRUS
Details: Recombinant AcMNPV (BacToBac, Invitrogen) viruses containing the Bombyx mori cytoplasmic virus polyhedrin gene were amplified in Sf9 cells in suspension culture.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 50 MDa / Experimental value: NO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9 / Plasmid: Bacmid
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Lepidoptera
Virus shellName: Nucleocapsid / Diameter: 500 nm
Buffer solutionpH: 8.7 / Details: 50 mM Tris, 0.5 mM EDTA, pH 8.7
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HClNH2C(CH2OH)3.HCl1
20.5 mMEthylenedinitrilotetraacetic acid (EDTA)(HO2CCH2)2NCH2CH2N(CH2CO2H)21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: A suspension of AcMNPV viruses was purified from cell culture supernatant using sucrose gradient ultracentrifugation. Sucrose was removed after purification through dialysis.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Grid was blotted using zero incubation time, blot time of 2 s, blot force of -10 and drain time of 1 s.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 14 sec. / Electron dose: 47.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1847
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansMovie frames/image: 70 / Used frames/image: 1-70

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.1.2particle selection
2EMAN22.2particle selectione2helixboxer.py
3RELION2.1particle selection
4EPU1image acquisition
6cryoSPARC4.1.2CTF correction
9UCSF ChimeraX1.5model fitting
10Coot0.9.8.6model fitting
12PHENIX1.20.1_4487model refinementphenix.real_space_refine
13SPRING0.84.1470initial Euler assignmentUsed for Fourier-Bessel indexing
14RELION2.1initial Euler assignmentUsed to test helical and cyclic symmetries
15cryoSPARC4.1.2final Euler assignment
16cryoSPARC4.1.2classification
17cryoSPARC4.1.23D reconstruction
Image processingDetails: The movies were imported into cryoSPARC and binned two times by Fourier cropping, and subjected to motion correction and CTF estimation using patch motion correction and patch CTF estimation
CTF correctionDetails: Defocus values were estimated using patch CTF estimation, and CTF correction was performed during 3D reconstruction
Type: NONE
Particle selectionNum. of particles selected: 2165694
Details: Manually selected particles in EMAN2 were used to create a 2D template in cryoSPARC for automated filament tracing resulting in 77,356 particles. After helical refinement and symmetry ...Details: Manually selected particles in EMAN2 were used to create a 2D template in cryoSPARC for automated filament tracing resulting in 77,356 particles. After helical refinement and symmetry expansion, 2,165,694 subparticles were extracted.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1002951 / Algorithm: BACK PROJECTION
Details: Final reconstruction was generated using local refinement in cryoSPARC.
Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: ChimeraX was used to perform rigid-body fitting of an AlphaFold2 model. Flexible modeling was performed using Coot and refined in Phenix.
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319269
ELECTRON MICROSCOPYf_angle_d0.45126103
ELECTRON MICROSCOPYf_dihedral_angle_d4.4842572
ELECTRON MICROSCOPYf_chiral_restr0.0412873
ELECTRON MICROSCOPYf_plane_restr0.0033460

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