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- EMDB-43590: The cap complex of the baculovirus nucleocapsid (Autographa calif... -

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Basic information

Entry
Database: EMDB / ID: EMD-43590
TitleThe cap complex of the baculovirus nucleocapsid (Autographa californica multiple nucleopolyhedrovirus)
Map data
Sample
  • Virus: Autographa californica multiple nucleopolyhedrovirus
KeywordsNucleocapsid / Cap / baculovirus / virus / AcMNPV / VP39
Biological speciesAutographa californica multiple nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsJohnstone BA / Koszalka P / Venugopal H / Coulibaly F
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103388 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_43590.png

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Map

FileDownload / File: emd_43590.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 700 pix.
= 987. Å		1.41 Å/pix.
x 700 pix.
= 987. Å		1.41 Å/pix.
x 700 pix.
= 987. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
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Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.3384154 - 1.0477558
Average (Standard dev.)0.002426795 (±0.056982744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 987.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43590_msk_1.map
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Additional map: Sharpened map

Fileemd_43590_additional_1.map
AnnotationSharpened map
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Half map: Half map A

Fileemd_43590_half_map_1.map
AnnotationHalf map A
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Half map: Half map B

Fileemd_43590_half_map_2.map
AnnotationHalf map B
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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

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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)
Virus shellShell ID: 1 / Name: Nucleocapsid / Diameter: 500.0 Å

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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: 7.4 / Details: 10 mM HEPES pH 7.4, 500 mM potassium chloride
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11439 / Average electron dose: 50.0 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: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 143933
Details: Particles were picked using a trained Topaz model, trained using manual picking of nucleocapsid ends from 700 micrographs
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionApplied symmetry - Point group: C14 (14 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.1.2) / Number images used: 8557
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.1.2)
FSC plot (resolution estimation)

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