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- PDB-8vwi: The base complex of the AcMNPV baculovirus nucleocapsid (Class 1,... -

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Basic information

Entry
Database: PDB / ID: 8vwi
TitleThe base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction)
Components
  • 38K (AC98) protein in P143-LEF5 intergenic region
  • 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: 4.71 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: To Be Published
Title: The baculovirus structure defines the hallmarks of a new viral realm
Authors: Johnstone, B.A. / Hardy, J.M. / Ha, J. / Butkovic, A. / Koszalka, P. / Accurso, C. / Venugopal, H. / de Marco, A. / Krupovic, M. / Coulibaly, F.
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

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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) protein in P143-LEF5 intergenic region
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) protein in P143-LEF5 intergenic region
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
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 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41700
#7: Protein 38K (AC98) protein in P143-LEF5 intergenic region / ORF2


Mass: 38070.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Cell line (production host): Sf9 / 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
11cryoSPARC4.1.2initial Euler assignment
12cryoSPARC4.1.2final Euler assignment
14cryoSPARC4.1.23D reconstruction
15PHENIX1.20.1model refinement
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: 4.71 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
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 270 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002780301
ELECTRON MICROSCOPYf_angle_d0.6028108624
ELECTRON MICROSCOPYf_chiral_restr0.0412150
ELECTRON MICROSCOPYf_plane_restr0.006613999
ELECTRON MICROSCOPYf_dihedral_angle_d13.843530070

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