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- PDB-9h2h: AcMNPV apical cap - composite map of the C2 plug -

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Basic information

Entry
Database: PDB / ID: 9h2h
TitleAcMNPV apical cap - composite map of the C2 plug
Components
  • (DNA (58-MER)) x 2
  • Occlusion-derived virus envelope protein E27
  • Protein AC54
  • Protein C42
KeywordsVIRUS / nucleocapsid
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / virion component / viral envelope / host cell nucleus / virion membrane / membrane
Similarity search - Function
Baculovirus VP1054 / Baculovirus VP1054 protein / Baculovirus occlusion-derived virus envelope EC27 / Baculovirus occlusion-derived virus envelope protein EC27 / Autographa californica nuclear polyhedrosis virus (AcMNPV), C42 / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C42 / Protein AC54 / Occlusion-derived virus envelope protein E27
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsEffantin, G. / Kandiah, E. / Pelosse, M.
Funding support1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AC54
B: Protein AC54
C: Protein AC54
D: Protein AC54
E: DNA (58-MER)
F: DNA (58-MER)
G: Occlusion-derived virus envelope protein E27
H: Occlusion-derived virus envelope protein E27
I: Protein C42
J: Protein C42
K: Occlusion-derived virus envelope protein E27
L: Occlusion-derived virus envelope protein E27
M: Protein C42
N: Protein C42
O: Occlusion-derived virus envelope protein E27
P: Occlusion-derived virus envelope protein E27
Q: Protein C42
R: Protein C42
S: Occlusion-derived virus envelope protein E27
T: Occlusion-derived virus envelope protein E27
U: Protein C42
V: Protein C42


Theoretical massNumber of molelcules
Total (without water)805,55122
Polymers805,55122
Non-polymers00
Water00
1
A: Protein AC54
B: Protein AC54
C: Protein AC54
D: Protein AC54
E: DNA (58-MER)
F: DNA (58-MER)
G: Occlusion-derived virus envelope protein E27
H: Occlusion-derived virus envelope protein E27
I: Protein C42
J: Protein C42
K: Occlusion-derived virus envelope protein E27
L: Occlusion-derived virus envelope protein E27
M: Protein C42
N: Protein C42
O: Occlusion-derived virus envelope protein E27
P: Occlusion-derived virus envelope protein E27
Q: Protein C42
R: Protein C42
S: Occlusion-derived virus envelope protein E27
T: Occlusion-derived virus envelope protein E27
U: Protein C42
V: Protein C42

A: Protein AC54
B: Protein AC54
C: Protein AC54
D: Protein AC54
E: DNA (58-MER)
F: DNA (58-MER)
G: Occlusion-derived virus envelope protein E27
H: Occlusion-derived virus envelope protein E27
I: Protein C42
J: Protein C42
K: Occlusion-derived virus envelope protein E27
L: Occlusion-derived virus envelope protein E27
M: Protein C42
N: Protein C42
O: Occlusion-derived virus envelope protein E27
P: Occlusion-derived virus envelope protein E27
Q: Protein C42
R: Protein C42
S: Occlusion-derived virus envelope protein E27
T: Occlusion-derived virus envelope protein E27
U: Protein C42
V: Protein C42


Theoretical massNumber of molelcules
Total (without water)1,611,10144
Polymers1,611,10144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1

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Components

#1: Protein
Protein AC54


Mass: 42151.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41458
#2: DNA chain DNA (58-MER)


Mass: 17953.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
#3: DNA chain DNA (58-MER)


Mass: 17778.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
#4: Protein
Occlusion-derived virus envelope protein E27 / ODV-E27


Mass: 33568.152 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41702
#5: Protein
Protein C42 / C42 / P40


Mass: 41583.594 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P25695
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Autographa californica nucleopolyhedrovirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12477 / Symmetry type: POINT

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