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- PDB-8taf: Autographa californica multiple nucleopolyhedrovirus VP39 -

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Basic information

Entry
Database: PDB / ID: 8taf
TitleAutographa californica multiple nucleopolyhedrovirus VP39
ComponentsMajor viral capsid protein
KeywordsVIRAL PROTEIN / nucleocapsid protein VP39
Function / homologyBaculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / viral capsid / structural molecule activity / Major viral capsid protein
Function and homology information
Biological speciesAutographa californica multiple nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBenning, F.M.C. / Chao, L.H.
Funding support United States, Switzerland, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142553 United States
Swiss National Science FoundationP180777 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130289 United States
CitationJournal: Nat Commun / Year: 2024
Title: Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly.
Authors: Friederike M C Benning / Simon Jenni / Coby Y Garcia / Tran H Nguyen / Xuewu Zhang / Luke H Chao /
Abstract: Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which ...Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We use electron cryomicroscopy to determine a 3.2 Å helical reconstruction of an infectious nucleocapsid of Autographa californica multiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a distinct protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism shows that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly.
History
DepositionJun 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 10, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Major viral capsid protein
L: Major viral capsid protein
M: Major viral capsid protein
N: Major viral capsid protein
O: Major viral capsid protein
P: Major viral capsid protein
Q: Major viral capsid protein
R: Major viral capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,87116
Polymers286,3478
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major viral capsid protein / VP39


Mass: 35793.422 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: Ac-vp39, LO84_090 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0N6WHR0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Autographa californica multiple nucleopolyhedrovirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -1900 nm / Nominal defocus min: -400 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
2SerialEM3.8.5image acquisition
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -7.16 ° / Axial rise/subunit: 43.86 Å / Axial symmetry: D14
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4983 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320364
ELECTRON MICROSCOPYf_angle_d0.53827590
ELECTRON MICROSCOPYf_dihedral_angle_d4.4342748
ELECTRON MICROSCOPYf_chiral_restr0.0433030
ELECTRON MICROSCOPYf_plane_restr0.0043665

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