8VWH

Structure of the baculovirus major nucleocapsid protein VP39 (localised reconstruction)

• PDB DOI: https://doi.org/10.2210/pdb8VWH/pdb
• EM Map EMD-43586: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Autographa californica multiple nucleopolyhedrovirus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-02-01 Released: 2024-11-06 
• Deposition Author(s): Johnstone, B.A., Hardy, J.M., Ha, J.H., Venugopal, H., Coulibaly, F.
• Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

The baculovirus structure defines 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.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 312.39 kDa 
• Atom Count: 18,889 
• Modelled Residue Count: 2,329 
• Deposited Residue Count: 2,776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K], G [auth M], H [auth O]	347	Autographa californica multiple nucleopolyhedrovirus	Mutation(s): 0  Gene Names: P39, VP39, ORF89
UniProt
Find proteins for P17499 (Autographa californica nuclear polyhedrosis virus) Explore P17499  Go to UniProtKB:  P17499

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth A], J [auth C], K [auth E], L [auth G], M [auth I], N [auth K], O [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC	4.1.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Johnstone, B.A., Hardy, J.M., Ha, J.H., Venugopal, H., Coulibaly, F.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP210103388
National Health and Medical Research Council (NHMRC, Australia)	Australia	2008096

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection