9H2A | pdb_00009h2a

AcMNPV complete basal cap


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of AcMNPV nucleocapsid reveals DNA portal organization and packaging apparatus of circular dsDNA baculovirus.

Effantin, G.Kandiah, E.Pelosse, M.

(2025) Nat Commun 16: 4844-4844

  • DOI: https://doi.org/10.1038/s41467-025-60152-2
  • Primary Citation of Related Structures:  
    9H1S, 9H2A, 9H2B, 9H2C, 9H2H, 9H2J, 9H2K

  • PubMed 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 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.


  • Organizational Affiliation

    Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France. gregory.effantin@ibs.fr.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Occlusion-derived virus envelope protein E27
A, B, O, P, Q
A, B, O, P, Q, R
290Autographa californica nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for P41702 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP41702
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein C42
C, D, S, T, U
C, D, S, T, U, V
361Autographa californica nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for P25695 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP25695
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region
E, W
320Autographa californica nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for P24745 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP24745
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AC142
F, X
477Autographa californica nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for P41700 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP41700
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein347Autographa californica nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for P17499 (Autographa californica nuclear polyhedrosis virus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid-associated protein VP80691Autographa californica nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for Q00733 (Autographa californica nuclear polyhedrosis virus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AC109DA [auth d],
L
390Autographa californica nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for P41662 (Autographa californica nuclear polyhedrosis virus)
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
GA [auth G]
HA [auth H]
IA [auth M]
JA [auth N]
KA [auth Y]
GA [auth G],
HA [auth H],
IA [auth M],
JA [auth N],
KA [auth Y],
LA [auth Z],
MA [auth e],
NA [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release