8VWJ | pdb_00008vwj

The base complex of the AcMNPV baculovirus nucleocapsid (Class 2, localised reconstruction)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The nucleocapsid architecture and structural atlas of the prototype baculovirus define the hallmarks of a new viral realm.

Johnstone, B.A.Hardy, J.M.Ha, J.Butkovic, A.Koszalka, P.Accurso, C.Venugopal, H.de Marco, A.Krupovic, M.Coulibaly, F.

(2024) Sci Adv 10: eado2631-eado2631

  • DOI: https://doi.org/10.1126/sciadv.ado2631
  • Primary Citation of Related Structures:  
    8VWH, 8VWJ

  • PubMed Abstract: 

    Baculovirus is the most studied insect virus owing to a broad ecological distribution and ease of engineering for biotechnological applications. However, its structure and evolutionary place in the virosphere remain enigmatic. Using cryo-electron microscopy, we show that the nucleocapsid forms a covalently cross-linked helical tube protecting a highly compacted 134-kilobase pair DNA genome. The ends of the tube are sealed by the base and cap substructures, which share a 126-subunit hub but differ in components that promote actin tail-mediated propulsion and nuclear entry of the nucleocapsid, respectively. Unexpectedly, sensitive searches for hidden evolutionary links show that the morphogenetic machinery and conserved oral infectivity factors originated within the lineage of baculo-like viruses (class Naldaviricetes ). The unique viral architecture and structural atlas of hallmark proteins firmly place these viruses into a separate new realm, the highest taxonomy rank, and provide a structural framework to expand their use as sustainable bioinsecticides and biomedical tools.


  • Organizational Affiliation
    • Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein347Autographa californica multiple nucleopolyhedrovirusMutation(s): 0 
Gene Names: P39VP39ORF89
UniProt
Find proteins for P17499 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP17499
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid-associated protein VP80691Autographa californica multiple nucleopolyhedrovirusMutation(s): 0 
Gene Names: VP80ORF104
UniProt
Find proteins for Q00733 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupQ00733
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Occlusion-derived virus envelope protein E27290Autographa californica multiple nucleopolyhedrovirusMutation(s): 0 
Gene Names: E27ORF144
UniProt
Find proteins for P41702 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP41702
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein C42361Autographa californica multiple nucleopolyhedrovirusMutation(s): 0 
Gene Names: ORF101
UniProt
Find proteins for P25695 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP25695
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AC109HA [auth i],
N
390Autographa californica multiple nucleopolyhedrovirusMutation(s): 0 
Gene Names: ORF109
UniProt
Find proteins for P41662 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP41662
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AC142IA [auth j],
O
477Autographa californica multiple nucleopolyhedrovirusMutation(s): 0 
Gene Names: ORF142
UniProt
Find proteins for P41700 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP41700
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
38K (AC98)JA [auth k],
P
320Autographa californica multiple nucleopolyhedrovirusMutation(s): 0 
UniProt
Find proteins for P24745 (Autographa californica nuclear polyhedrosis virus)
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UniProt GroupP24745
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
KA [auth A]
LA [auth B]
MA [auth C]
NA [auth D]
OA [auth E]
KA [auth A],
LA [auth B],
MA [auth C],
NA [auth D],
OA [auth E],
PA [auth F],
QA [auth V],
RA [auth W],
SA [auth X],
TA [auth Y],
UA [auth Z],
VA [auth a]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC4.1.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP210103388

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection
  • Version 1.2: 2025-05-21
    Changes: Data collection, Database references