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- PDB-9h2a: AcMNPV complete basal cap -

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Basic information

Entry
Database: PDB / ID: 9h2a
TitleAcMNPV complete basal cap
Components
  • Capsid-associated protein VP80
  • Major capsid protein
  • Occlusion-derived virus envelope protein E27
  • Protein AC109
  • Protein AC142
  • Protein C42
  • Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region
KeywordsVIRUS / nucleocapsid
Function / homology
Function and homology information


transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / symbiont-mediated perturbation of host cell cycle progression / nuclear capsid assembly / virion component / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm ...transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / symbiont-mediated perturbation of host cell cycle progression / nuclear capsid assembly / virion component / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm / viral envelope / host cell nucleus / virion membrane / structural molecule activity / protein homodimerization activity / DNA binding / membrane
Similarity search - Function
Protein of unknown function DUF694 / Protein of unknown function (DUF705) / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / HAD-superfamily phosphatase, subfamily IIIC / Baculovirus occlusion-derived virus envelope EC27 ...Protein of unknown function DUF694 / Protein of unknown function (DUF705) / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / HAD-superfamily phosphatase, subfamily IIIC / 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 / Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Major capsid protein / Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region / Protein C42 / Protein AC109 / Protein AC142 / Occlusion-derived virus envelope protein E27 / Capsid-associated protein VP80
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 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: Occlusion-derived virus envelope protein E27
B: Occlusion-derived virus envelope protein E27
C: Protein C42
D: Protein C42
E: Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region
F: Protein AC142
G: Major capsid protein
H: Major capsid protein
I: Capsid-associated protein VP80
J: Capsid-associated protein VP80
K: Capsid-associated protein VP80
L: Protein AC109
M: Major capsid protein
N: Major capsid protein
O: Occlusion-derived virus envelope protein E27
P: Occlusion-derived virus envelope protein E27
Q: Occlusion-derived virus envelope protein E27
R: Occlusion-derived virus envelope protein E27
S: Protein C42
T: Protein C42
U: Protein C42
V: Protein C42
W: Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region
X: Protein AC142
Y: Major capsid protein
Z: Major capsid protein
a: Capsid-associated protein VP80
b: Capsid-associated protein VP80
c: Capsid-associated protein VP80
d: Protein AC109
e: Major capsid protein
f: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,520,01540
Polymers1,519,49232
Non-polymers5238
Water00
1
A: Occlusion-derived virus envelope protein E27
B: Occlusion-derived virus envelope protein E27
C: Protein C42
D: Protein C42
E: Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region
F: Protein AC142
G: Major capsid protein
H: Major capsid protein
I: Capsid-associated protein VP80
J: Capsid-associated protein VP80
K: Capsid-associated protein VP80
L: Protein AC109
M: Major capsid protein
N: Major capsid protein
O: Occlusion-derived virus envelope protein E27
P: Occlusion-derived virus envelope protein E27
Q: Occlusion-derived virus envelope protein E27
R: Occlusion-derived virus envelope protein E27
S: Protein C42
T: Protein C42
U: Protein C42
V: Protein C42
W: Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region
X: Protein AC142
Y: Major capsid protein
Z: Major capsid protein
a: Capsid-associated protein VP80
b: Capsid-associated protein VP80
c: Capsid-associated protein VP80
d: Protein AC109
e: Major capsid protein
f: Major capsid protein
hetero molecules
x 7


Theoretical massNumber of molelcules
Total (without water)10,640,106280
Polymers10,636,443224
Non-polymers3,66356
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation6
SymmetryPoint symmetry: (Schoenflies symbol: C7 (7 fold cyclic))

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Components

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Protein , 7 types, 32 molecules ABOPQRCDSTUVEWFXGHMNYZefIJKabcLd

#1: Protein
Occlusion-derived virus envelope protein E27 / ODV-E27


Mass: 33568.152 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41702
#2: Protein
Protein C42 / C42 / P40


Mass: 41583.594 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P25695
#3: Protein Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region / ORF2


Mass: 38070.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P24745
#4: Protein Protein AC142


Mass: 55480.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41700
#5: Protein
Major capsid protein


Mass: 38991.109 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P17499
#6: Protein
Capsid-associated protein VP80


Mass: 79974.469 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: Q00733
#7: Protein Protein AC109


Mass: 44851.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41662

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Non-polymers , 1 types, 8 molecules

#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: #1-#7 / 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: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35066 / Symmetry type: POINT

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