+Open data
-Basic information
Entry | Database: PDB / ID: 8taf | ||||||||||||
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Title | Autographa californica multiple nucleopolyhedrovirus VP39 | ||||||||||||
Components | Major viral capsid protein | ||||||||||||
Keywords | VIRAL PROTEIN / nucleocapsid protein VP39 | ||||||||||||
Function / homology | Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / viral capsid / structural molecule activity / Major viral capsid protein Function and homology information | ||||||||||||
Biological species | Autographa californica multiple nucleopolyhedrovirus | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Benning, F.M.C. / Chao, L.H. | ||||||||||||
Funding support | United States, Switzerland, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8taf.cif.gz | 909.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8taf.ent.gz | 773.3 KB | Display | PDB format |
PDBx/mmJSON format | 8taf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8taf_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8taf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8taf_validation.xml.gz | 72.9 KB | Display | |
Data in CIF | 8taf_validation.cif.gz | 106.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/8taf ftp://data.pdbj.org/pub/pdb/validation_reports/ta/8taf | HTTPS FTP |
-Related structure data
Related structure data | 41133MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Autographa californica multiple nucleopolyhedrovirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Autographa californica multiple nucleopolyhedrovirus |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -1900 nm / Nominal defocus min: -400 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
EM software | Name: SerialEM / Version: 3.8.5 / Category: image acquisition | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -7.16 ° / Axial rise/subunit: 43.86 Å / Axial symmetry: D14 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4983 / Symmetry type: HELICAL | ||||||||||||||||||||||||
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