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- PDB-8vwj: The base complex of the AcMNPV baculovirus nucleocapsid (Class 2,... -

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Basic information

Entry
Database: PDB / ID: 8vwj
TitleThe base complex of the AcMNPV baculovirus nucleocapsid (Class 2, localised reconstruction)
Components
  • 38K (AC98)
  • Capsid-associated protein VP80
  • Major capsid protein
  • Occlusion-derived virus envelope protein E27
  • Protein AC109
  • Protein AC142
  • Protein C42
KeywordsVIRAL PROTEIN / Nucleocapsid / Base / baculovirus / virus / AcMNPV / VP39
Function / homology
Function and homology information


transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / nuclear capsid assembly / symbiont-mediated perturbation of host cell cycle progression / virion component / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm ...transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / nuclear capsid assembly / symbiont-mediated perturbation of host cell cycle progression / virion component / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm / viral envelope / host cell nucleus / virion membrane / structural molecule activity / protein homodimerization activity / DNA binding / membrane
Similarity search - Function
Protein of unknown function DUF694 / Protein of unknown function (DUF705) / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / HAD-superfamily phosphatase, subfamily IIIC / Baculovirus occlusion-derived virus envelope EC27 ...Protein of unknown function DUF694 / Protein of unknown function (DUF705) / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / HAD-superfamily phosphatase, subfamily IIIC / Baculovirus occlusion-derived virus envelope EC27 / Baculovirus occlusion-derived virus envelope protein EC27 / Autographa californica nuclear polyhedrosis virus (AcMNPV), C42 / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101 / Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Major capsid protein / Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region / Protein C42 / Protein AC109 / Protein AC142 / Occlusion-derived virus envelope protein E27 / Capsid-associated protein VP80
Similarity search - Component
Biological speciesAutographa californica multiple nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.78 Å
AuthorsJohnstone, B.A. / Koszalka, P. / Ha, J. / Venugopal, H. / Coulibaly, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103388 Australia
CitationJournal: Sci Adv / Year: 2024
Title: The nucleocapsid architecture and structural atlas of the prototype baculovirus define the hallmarks of a new viral realm.
Authors: Bronte A Johnstone / Joshua M Hardy / Jungmin Ha / Anamarija Butkovic / Paulina Koszalka / Cathy Accurso / Hariprasad Venugopal / Alex de Marco / Mart Krupovic / Fasséli Coulibaly /
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 ...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 ). 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.
History
DepositionFeb 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2May 21, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Capsid-associated protein VP80
H: Capsid-associated protein VP80
I: Capsid-associated protein VP80
J: Occlusion-derived virus envelope protein E27
K: Protein C42
L: Protein C42
M: Occlusion-derived virus envelope protein E27
N: Protein AC109
O: Protein AC142
P: 38K (AC98)
Q: Occlusion-derived virus envelope protein E27
R: Protein C42
S: Occlusion-derived virus envelope protein E27
T: Protein C42
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Major capsid protein
Z: Major capsid protein
a: Major capsid protein
b: Capsid-associated protein VP80
c: Capsid-associated protein VP80
d: Capsid-associated protein VP80
e: Occlusion-derived virus envelope protein E27
f: Protein C42
g: Protein C42
h: Occlusion-derived virus envelope protein E27
i: Protein AC109
j: Protein AC142
k: 38K (AC98)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,676,24148
Polymers1,675,45636
Non-polymers78512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 36 molecules ABCDEFVWXYZaGHIbcdJMQSehKLRTfg...

#1: Protein
Major capsid protein


Mass: 38991.109 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: P39, VP39, ORF89 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17499
#2: Protein
Capsid-associated protein VP80


Mass: 79974.469 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: VP80, ORF104 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00733
#3: Protein
Occlusion-derived virus envelope protein E27 / ODV-E27


Mass: 33568.152 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: E27, ORF144 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41702
#4: Protein
Protein C42 / C42 / P40


Mass: 41583.594 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: ORF101 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25695
#5: Protein Protein AC109


Mass: 44851.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: ORF109 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41662
#6: Protein Protein AC142


Mass: 55480.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: ORF142 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41700
#7: Protein 38K (AC98) / ORF2


Mass: 38070.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24745

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Non-polymers , 1 types, 12 molecules

#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Autographa californica multiple nucleopolyhedrovirus / Type: VIRUS
Details: Recombinant AcMNPV (BacToBac, Invitrogen) viruses containing the Bombyx mori cytoplasmic virus polyhedrin gene were amplified in Sf9 cells in suspension culture.
Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: Bacmid
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Lepidoptera
Virus shellName: Nucleocapsid / Diameter: 500 nm
Buffer solutionpH: 7.4 / Details: 10 mM HEPES pH 7.4, 500 mM potassium chloride
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: A suspension of AcMNPV viruses was purified from cell culture supernatant using sucrose gradient ultracentrifugation. Sucrose was removed after purification through dialysis.
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11439

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
4cryoSPARC4.1.2CTF correction
7Coot0.9.8.6model fitting
8UCSF ChimeraX1.5model fitting
9ISOLDEmodel fitting
11PHENIX1.20.1model refinement
12cryoSPARC4.1.2initial Euler assignment
13cryoSPARC4.1.2final Euler assignment
15cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 143933
Details: Particles were picked using a trained Topaz model, trained using manual picking of nucleocapsid ends from 700 micrographs
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53750 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE

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