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- EMDB-43585: Structure of the AcMNPV baculovirus VP39 nucleocapsid (C14 helica... -

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Basic information

Entry
Database: EMDB / ID: EMD-43585
TitleStructure of the AcMNPV baculovirus VP39 nucleocapsid (C14 helical reconstruction)
Map dataRefinement map
Sample
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Complex: C14 reconstruction of the helical portion of the nucleocapsid formed by dimers of VP39
      • Protein or peptide: Major nucleocapsid protein VP39 of Autographa californica multiple nucleopolyhedrovirus
KeywordsCapsid / helical assembly / virus / VP39 / nucleocapsid / 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
Methodhelical reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsHardy JM / Johnstone BA / 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_43585.png

Downloads & links

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Map

FileDownload / File: emd_43585.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 700 pix.
= 938. Å		1.34 Å/pix.
x 700 pix.
= 938. Å		1.34 Å/pix.
x 700 pix.
= 938. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.10064122 - 0.45826024
Average (Standard dev.)0.0062800446 (±0.034065872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 938.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43585_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_43585_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_43585_half_map_2.map
AnnotationHalf Map B
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
    • Complex: C14 reconstruction of the helical portion of the nucleocapsid formed by dimers of VP39
      • Protein or peptide: Major nucleocapsid protein VP39 of Autographa californica multiple nucleopolyhedrovirus

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Supramolecule #1: Autographa californica multiple nucleopolyhedrovirus

SupramoleculeName: Autographa californica multiple nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
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 (butterflies and moths)
Molecular weightTheoretical: 126.2 kDa/nm
Virus shellShell ID: 1 / Name: Nucleocapsid / Diameter: 500.0 Å

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Supramolecule #2: C14 reconstruction of the helical portion of the nucleocapsid for...

SupramoleculeName: C14 reconstruction of the helical portion of the nucleocapsid formed by dimers of VP39
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus

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Macromolecule #1: Major nucleocapsid protein VP39 of Autographa californica multipl...

MacromoleculeName: Major nucleocapsid protein VP39 of Autographa californica multiple nucleopolyhedrovirus
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical 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
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 43.22 Å
Applied symmetry - Helical parameters - Δ&Phi: -18.56 °
Applied symmetry - Helical parameters - Axial symmetry: C14 (14 fold cyclic)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 63596
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
Segment selectionNumber selected: 2165694
Software:
Namedetails
cryoSPARC (ver. 4.1.2)
EMAN2 (ver. 2.2)e2helixboxer.py
RELION (ver. 2.1)

Details: Manually selected particles in EMAN2 were used to create a 2D template in cryoSPARC for automated filament tracing resulting in 77,356 particles.
Startup modelType of model: OTHER
Details: A sub-tomogram average reconstruction was used as an initial reference for helical reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Details: Final reconstruction was generated using the Helical Refinement job in cryoSPARC with cyclic and helical symmetry applied (C14, a rise 43.22 angstroms, and a twist of -18.56)
FSC plot (resolution estimation)

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