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- EMDB-51771: AcMNPV helical nucleocapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-51771
TitleAcMNPV helical nucleocapsid
Map dataAcMNPV helical nucleocapsid
Sample
  • Virus: Autographa californica nucleopolyhedrovirus
    • Protein or peptide: Major capsid protein
  • Ligand: ZINC ION
Keywordsnucleocapsid / helical / VIRUS
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 nucleopolyhedrovirus
Methodhelical reconstruction / cryo EM / Resolution: 3.0 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 10, 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_51771.png

Downloads & links

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Map

FileDownload / File: emd_51771.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcMNPV helical nucleocapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 500 pix.
= 675. Å		1.35 Å/pix.
x 500 pix.
= 675. Å		1.35 Å/pix.
x 500 pix.
= 675. 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: 0.005
Minimum - Maximum-0.011736907 - 0.026616992
Average (Standard dev.)0.00021022082 (±0.0016764615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 675.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51771_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: AcMNPV helical nucleocapsid - half map 2

Fileemd_51771_half_map_1.map
AnnotationAcMNPV helical nucleocapsid - half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AcMNPV helical nucleocapsid - half map 1

Fileemd_51771_half_map_2.map
AnnotationAcMNPV helical nucleocapsid - 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
    • Protein or peptide: Major capsid protein
  • Ligand: ZINC ION

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Supramolecule #1: Autographa californica nucleopolyhedrovirus

SupramoleculeName: Autographa californica nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / 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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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 38.991109 KDa
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: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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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

Final reconstructionApplied symmetry - Helical parameters - Δz: 42.57 Å
Applied symmetry - Helical parameters - Δ&Phi: -7.11 °
Applied symmetry - Helical parameters - Axial symmetry: C14 (14 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138225
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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