8VWI | pdb_00008vwi

The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction)

PDB DOI: https://doi.org/10.2210/pdb8VWI/pdb
EM Map EMD-43588: 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., Koszalka, P., Ha, J., Venugopal, H., Coulibaly, F.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.71 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 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 1,676.24 kDa
Atom Count: 78,647
Modeled Residue Count: 9,602
Deposited Residue Count: 14,590
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A B C D E A, B, C, D, E, F, U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17499
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid-associated protein VP80	AA [auth b] BA [auth c] CA [auth d] G H AA [auth b], BA [auth c], CA [auth d], G, H, I	691	Autographa californica multiple nucleopolyhedrovirus	Mutation(s): 0 Gene Names: VP80, ORF104
UniProt
Find proteins for Q00733 (Autographa californica nuclear polyhedrosis virus) Explore Q00733 Go to UniProtKB: Q00733
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00733
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Occlusion-derived virus envelope protein E27	DA [auth e] GA [auth h] J M Q DA [auth e], GA [auth h], J, M, Q, S	290	Autographa californica multiple nucleopolyhedrovirus	Mutation(s): 0 Gene Names: E27, ORF144
UniProt
Find proteins for P41702 (Autographa californica nuclear polyhedrosis virus) Explore P41702 Go to UniProtKB: P41702
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41702
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein C42	EA [auth f] FA [auth g] K L R EA [auth f], FA [auth g], K, L, R, T	361	Autographa californica multiple nucleopolyhedrovirus	Mutation(s): 0 Gene Names: ORF101
UniProt
Find proteins for P25695 (Autographa californica nuclear polyhedrosis virus) Explore P25695 Go to UniProtKB: P25695
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25695
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AC109	HA [auth i], N	390	Autographa californica multiple nucleopolyhedrovirus	Mutation(s): 0 Gene Names: ORF109
UniProt
Find proteins for P41662 (Autographa californica nuclear polyhedrosis virus) Explore P41662 Go to UniProtKB: P41662
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41662
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AC142	IA [auth j], O	477	Autographa californica multiple nucleopolyhedrovirus	Mutation(s): 0 Gene Names: ORF142
UniProt
Find proteins for P41700 (Autographa californica nuclear polyhedrosis virus) Explore P41700 Go to UniProtKB: P41700
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41700
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
38K (AC98) protein in P143-LEF5 intergenic region	JA [auth k], P	320	Autographa californica multiple nucleopolyhedrovirus	Mutation(s): 0
UniProt
Find proteins for P24745 (Autographa californica nuclear polyhedrosis virus) Explore P24745 Go to UniProtKB: P24745
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24745
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain VA [auth a] SDF format, chain UA [auth Z] SDF format, chain TA [auth Y] SDF format, chain SA [auth X] SDF format, chain RA [auth W] SDF format, chain QA [auth V] SDF format, chain PA [auth F] SDF format, chain OA [auth E] SDF format, chain NA [auth D] SDF format, chain MA [auth C] SDF format, chain LA [auth B] SDF format, chain KA [auth A] MOL2 format, chain VA [auth a] MOL2 format, chain UA [auth Z] MOL2 format, chain TA [auth Y] MOL2 format, chain SA [auth X] MOL2 format, chain RA [auth W] MOL2 format, chain QA [auth V] MOL2 format, chain PA [auth F] MOL2 format, chain OA [auth E] MOL2 format, chain NA [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth A] mmCIF format, chain VA [auth a] mmCIF format, chain UA [auth Z] mmCIF format, chain TA [auth Y] mmCIF format, chain SA [auth X] mmCIF format, chain RA [auth W] mmCIF format, chain QA [auth V] mmCIF format, chain PA [auth F] mmCIF format, chain OA [auth E] mmCIF format, chain NA [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth A]	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		Interactions Focus chain KA [auth A] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain OA [auth E] Focus chain PA [auth F] Focus chain QA [auth V] Focus chain RA [auth W] Focus chain SA [auth X] Focus chain TA [auth Y] Focus chain UA [auth Z] Focus chain VA [auth a] Interactions & Density Focus chain KA [auth A] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain OA [auth E] Focus chain PA [auth F] Focus chain QA [auth V] Focus chain RA [auth W] Focus chain SA [auth X] Focus chain TA [auth Y] Focus chain UA [auth Z] Focus chain VA [auth a]