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- EMDB-51806: AcMNPV apical cap - C2 plug only - focused map 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-51806
TitleAcMNPV apical cap - C2 plug only - focused map 1
Map dataAcMNPV apical cap - C2 plug body 1
Sample
  • Virus: Autographa californica nucleopolyhedrovirus
Keywordsnucleocapsid / VIRUS
Biological speciesAutographa californica nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsEffantin G / Kandiah E / Pelosse M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure of AcMNPV nucleocapsid reveals DNA portal organization and packaging apparatus of circular dsDNA baculovirus.
Authors: Gregory Effantin / Eaazhisai Kandiah / Martin Pelosse /
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 ...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.
History
DepositionOct 11, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51806.png

Downloads & links

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Map

FileDownload / File: emd_51806.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcMNPV apical cap - C2 plug body 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.012082941 - 0.02741965
Average (Standard dev.)-0.00014632511 (±0.0011413094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51806_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AcMNPV apical cap - C2 plug body 1 - half map 2

Fileemd_51806_half_map_1.map
AnnotationAcMNPV apical cap - C2 plug body 1 - half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AcMNPV apical cap - C2 plug body 1 - half map 1

Fileemd_51806_half_map_2.map
AnnotationAcMNPV apical cap - C2 plug body 1 - half map 1
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 nucleopolyhedrovirus

EntireName: Autographa californica nucleopolyhedrovirus
Components
  • Virus: Autographa californica nucleopolyhedrovirus

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Supramolecule #1: Autographa californica nucleopolyhedrovirus

SupramoleculeName: Autographa californica nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#15 / NCBI-ID: 46015
Sci species name: Autographa californica nucleopolyhedrovirus
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12477
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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