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- EMDB-43586: Structure of the baculovirus major nucleocapsid protein VP39 (loc... -

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Basic information

Entry
Database: EMDB / ID: EMD-43586
TitleStructure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)
Map dataStructure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)
Sample
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: Major capsid protein
  • Ligand: ZINC ION
KeywordsCapsid / helical assembly / VIRAL PROTEIN
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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsJohnstone BA / Hardy JM / Ha JH / Venugopal H / Coulibaly F
Funding support Australia, 2 items
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, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43586.png

Downloads & links

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Map

FileDownload / File: emd_43586.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 256 pix.
= 340.48 Å		1.33 Å/pix.
x 256 pix.
= 340.48 Å		1.33 Å/pix.
x 256 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-2.4036603 - 2.869338
Average (Standard dev.)0.004798008 (±0.06634347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_43586_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_43586_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Autographa californica multiple nucleopolyhedrovirus

EntireName: Autographa californica multiple nucleopolyhedrovirus
Components
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: Major capsid protein
  • Ligand: ZINC ION

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Supramolecule #1: Autographa californica multiple nucleopolyhedrovirus

SupramoleculeName: Autographa californica multiple nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Recombinant AcMNPV (BacToBac, Invitrogen) viruses containing the Bombyx mori cytoplasmic virus polyhedrin gene were amplified in Sf9 cells in suspension culture.
NCBI-ID: 307456
Sci species name: Autographa californica multiple nucleopolyhedrovirus
Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Lepidoptera (moths & butterflies)
Molecular weightTheoretical: 50 MDa
Virus shellShell ID: 1 / Name: Nucleocapsid / Diameter: 500.0 Å

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 38.991109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDDGWFICN NHLIKRFKMS KMVLPIFDED DNQFKMTIAR HLVGNKERG IKRILIPSAT NYQDVFNLNS MMQAEQLIFH LIYNNENAVN TICDNLKYTE GFTSNTQRVI HSVYATTKSI L DTTNPNTF ...String:
MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDDGWFICN NHLIKRFKMS KMVLPIFDED DNQFKMTIAR HLVGNKERG IKRILIPSAT NYQDVFNLNS MMQAEQLIFH LIYNNENAVN TICDNLKYTE GFTSNTQRVI HSVYATTKSI L DTTNPNTF CSRVSRDELR FFDVTNARAL RGGAGDQLFN NYSGFLQNLI RRAVAPEYLQ IDTEELRFRN CATCIIDETG LV ASVPDGP ELYNPIRSSD IMRSQPNRLQ IRNVLKFEGD TRELDRTLSG YEEYPTYVPL FLGYQIINSE NNFLRNDFIP RAN PNATLG GGAVAGPAPG VAGEAGGGIA V

UniProtKB: Major capsid protein

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.7
Component:
ConcentrationFormulaName
50.0 mMNH2C(CH2OH)3.HClTris-HCl
0.5 mM(HO2CCH2)2NCH2CH2N(CH2CO2H)2Ethylenedinitrilotetraacetic acid (EDTA)

Details: 50 mM Tris, 0.5 mM EDTA, pH 8.7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Grid was blotted using zero incubation time, blot time of 2 s, blot force of -10 and drain time of 1 s..
DetailsA suspension of AcMNPV viruses was purified from cell culture supernatant using sucrose gradient ultracentrifugation. Sucrose was removed after purification through dialysis.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-70 / Number grids imaged: 1 / Number real images: 1847 / Average exposure time: 14.0 sec. / Average electron dose: 47.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe 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
Particle selectionNumber 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.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.2)
Details: Defocus values were estimated using patch CTF estimation, and CTF correction was performed during 3D reconstruction
Type: NONE
Startup modelType of model: OTHER
Details: A sub-tomogram average reconstruction was used as an initial reference for helical reconstruction
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2)
Details: Final reconstruction was generated using local refinement in cryoSPARC.
Number images used: 1002951
Initial angle assignmentType: OTHER
Software:
Namedetails
SPRING (ver. 0.84.1470)Used for Fourier-Bessel indexing
RELION (ver. 2.1)Used to test helical and cyclic symmetries

Details: Helical symmetry determination was performed using Fourier-Bessel indexing and projection matching in SPRING. Reconstruction tests in RELION were used to refine the cyclical and helical ...Details: Helical symmetry determination was performed using Fourier-Bessel indexing and projection matching in SPRING. Reconstruction tests in RELION were used to refine the cyclical and helical symmetry values (C14, a rise 43.22 angstroms, and a twist of -18.56 degrees).
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final 3D classificationNumber classes: 5 / Avg.num./class: 433139 / Software - Name: cryoSPARC (ver. 4.1.2)
Details: 3D classification was performed without re-alignment of the subparticles
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsChimeraX was used to perform rigid-body fitting of an AlphaFold2 model. Flexible modeling was performed using Coot and refined in Phenix.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8vwh:
Structure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)

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