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- PDB-9h2j: AcMNPV apical cap - C14 anchor complex only -

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Basic information

Entry
Database: PDB / ID: 9h2j
TitleAcMNPV apical cap - C14 anchor complex only
Components
  • Capsid-associated protein VP80
  • Major capsid protein
  • Occlusion-derived virus envelope protein E27
  • Protein AC109
  • Protein AC142
  • Protein Ac66
  • Protein C42
  • Tyrosine-protein phosphatase
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 / polynucleotide 5'-phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity ...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 / polynucleotide 5'-phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / 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
Viral desmoplakin, N-terminal / Viral Desmoplakin N-terminus / 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 / Baculovirus occlusion-derived virus envelope EC27 / Baculovirus occlusion-derived virus envelope protein EC27 ...Viral desmoplakin, N-terminal / Viral Desmoplakin N-terminus / 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 / 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 / : / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Major capsid protein / Tyrosine-protein phosphatase / Protein C42 / Protein Ac66 / 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: 4.7 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

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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: Protein AC142
F: Major capsid protein
G: Major capsid protein
H: Capsid-associated protein VP80
I: Capsid-associated protein VP80
J: Capsid-associated protein VP80
K: Protein AC109
L: Major capsid protein
M: Major capsid protein
N: Protein Ac66
O: Tyrosine-protein phosphatase
P: Protein Ac66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)854,18019
Polymers853,98316
Non-polymers1963
Water00
1
A: Occlusion-derived virus envelope protein E27
B: Occlusion-derived virus envelope protein E27
C: Protein C42
D: Protein C42
E: Protein AC142
F: Major capsid protein
G: Major capsid protein
H: Capsid-associated protein VP80
I: Capsid-associated protein VP80
J: Capsid-associated protein VP80
K: Protein AC109
L: Major capsid protein
M: Major capsid protein
N: Protein Ac66
O: Tyrosine-protein phosphatase
P: Protein Ac66
hetero molecules
x 14


Theoretical massNumber of molelcules
Total (without water)11,958,516266
Polymers11,955,769224
Non-polymers2,74742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation13

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Components

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Protein , 8 types, 16 molecules ABCDEFGLMHIJKNPO

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


Mass: 33568.152 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P25695
#3: Protein Protein AC142


Mass: 55480.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41700
#4: Protein
Major capsid protein


Mass: 38991.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P17499
#5: Protein Capsid-associated protein VP80


Mass: 79974.469 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: Q00733
#6: Protein Protein AC109


Mass: 44851.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41662
#7: Protein Protein Ac66


Mass: 94073.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P41467
#8: Protein Tyrosine-protein phosphatase / BVP


Mass: 19312.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
References: UniProt: P24656, protein-tyrosine-phosphatase

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Non-polymers , 1 types, 3 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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-#8 / Source: NATURAL
Molecular weightExperimental value: NO
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
SymmetryPoint symmetry: C14 (14 fold cyclic)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8327 / Symmetry type: POINT

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