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- EMDB-41133: Autographa californica multiple nucleopolyhedrovirus VP39 -

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Basic information

Entry
Database: EMDB / ID: EMD-41133
TitleAutographa californica multiple nucleopolyhedrovirus VP39
Map data
Sample
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: Major viral capsid protein
  • Ligand: ZINC ION
Keywordsnucleocapsid protein VP39 / VIRAL PROTEIN
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
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBenning FMC / Chao LH
Funding support United States, Switzerland, 3 items
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, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41133.png

Downloads & links

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Map

FileDownload / File: emd_41133.map.gz / Format: CCP4 / Size: 23.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.041606452 - 0.059107758
Average (Standard dev.)0.0005354302 (±0.0070146937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin4412573
Dimensions276104213
Spacing104276213
CellA: 85.799995 Å / B: 227.69998 Å / C: 175.72499 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41133_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41133_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Autographa californica multiple nucleopolyhedrovirus

EntireName: Autographa californica multiple nucleopolyhedrovirus
Components
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: Major viral capsid protein
  • Ligand: ZINC ION

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Supramolecule #1: Autographa californica multiple nucleopolyhedrovirus

SupramoleculeName: Autographa californica multiple nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 307456
Sci species name: Autographa californica multiple nucleopolyhedrovirus
Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Major viral capsid protein

MacromoleculeName: Major viral capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 35.793422 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QMRVNRCIFA SIVSFDACIT YKSPCSPDAY HDDGWFICNN HLIKRFKMSK MVLPIFDEDD NQFKMTIARH LVGNKERGIK RILIPSATN YQDVFNLNSM MQAEQLIFHL IYNNENAVNT ICDNLKYTEG FTSNTQRVIH SVYATTKSIL DTTNPNTFCS R VSRDELRF ...String:
QMRVNRCIFA SIVSFDACIT YKSPCSPDAY HDDGWFICNN HLIKRFKMSK MVLPIFDEDD NQFKMTIARH LVGNKERGIK RILIPSATN YQDVFNLNSM MQAEQLIFHL IYNNENAVNT ICDNLKYTEG FTSNTQRVIH SVYATTKSIL DTTNPNTFCS R VSRDELRF FDVTNARALR GGAGDQLFNN YSGFLQNLIR RAVAPEYLQI DTEELRFRNC ATCIIDETGL VASVPDGPEL YN PIRSSDI MRSQPNRLQI RNVLKFEGDT RELDRTLSGY EEYPTYVPLF LGYQIINSEN NFLRNDFIPR ANP

UniProtKB: Major viral capsid protein

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -1.9000000000000001 µm / Nominal defocus min: -0.4 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 43.86 Å
Applied symmetry - Helical parameters - Δ&Phi: -7.16 °
Applied symmetry - Helical parameters - Axial symmetry: D14 (2x14 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4983

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