+Open data
-Basic information
Entry | Database: PDB / ID: 6wh3 | ||||||||||||||||||
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Title | Capsid structure of Penaeus monodon metallodensovirus at pH 8.2 | ||||||||||||||||||
Components | Penaeus monodon metallodensovirus major capsid protein | ||||||||||||||||||
Keywords | VIRUS LIKE PARTICLE / parvovirus / densovirus / Penaeus monodon / crustacean / pathogen / Parvovirinae / metallodensovirus / shrimp / prawn / capsid | ||||||||||||||||||
Biological species | Penaeus monodon metallodensovirus | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å | ||||||||||||||||||
Authors | Penzes, J.J. / Pham, H.T. / Chipman, P. / Bhattacharya, N. / McKenna, R. / Agbandje-McKenna, M. / Tijssen, P. | ||||||||||||||||||
Funding support | Canada, United States, 5items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Molecular biology and structure of a novel penaeid shrimp densovirus elucidate convergent parvoviral host capsid evolution. Authors: Judit J Pénzes / Hanh T Pham / Paul Chipman / Nilakshee Bhattacharya / Robert McKenna / Mavis Agbandje-McKenna / Peter Tijssen / Abstract: The giant tiger prawn () is a decapod crustacean widely reared for human consumption. Currently, viruses of two distinct lineages of parvoviruses (PVs, family ; subfamily ) infect penaeid shrimp. ...The giant tiger prawn () is a decapod crustacean widely reared for human consumption. Currently, viruses of two distinct lineages of parvoviruses (PVs, family ; subfamily ) infect penaeid shrimp. Here, a PV was isolated and cloned from Vietnamese specimens, designated metallodensovirus (PmMDV). This is the first member of a third divergent lineage shown to infect penaeid decapods. PmMDV has a transcription strategy unique among invertebrate PVs, using extensive alternative splicing and incorporating transcription elements characteristic of vertebrate-infecting PVs. The PmMDV proteins have no significant sequence similarity with other PVs, except for an SF3 helicase domain in its nonstructural protein. Its capsid structure, determined by cryoelectron microscopy to 3-Å resolution, has a similar surface morphology to densovirus, despite the lack of significant capsid viral protein (VP) sequence similarity. Unlike other PVs, PmMDV folds its VP without incorporating a βA strand and displayed unique multimer interactions, including the incorporation of a Ca cation, attaching the N termini under the icosahedral fivefold symmetry axis, and forming a basket-like pentamer helix bundle. While the PmMDV VP sequence lacks a canonical phospholipase A2 domain, the structure of an EDTA-treated capsid, determined to 2.8-Å resolution, suggests an alternative membrane-penetrating cation-dependent mechanism in its N-terminal region. PmMDV is an observed example of convergent evolution among invertebrate PVs with respect to host-driven capsid structure and unique as a PV showing a cation-sensitive/dependent basket structure for an alternative endosomal egress. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wh3.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6wh3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6wh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wh3_validation.pdf.gz | 934.1 KB | Display | wwPDB validaton report |
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Full document | 6wh3_full_validation.pdf.gz | 962.1 KB | Display | |
Data in XML | 6wh3_validation.xml.gz | 404.9 KB | Display | |
Data in CIF | 6wh3_validation.cif.gz | 548.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/6wh3 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/6wh3 | HTTPS FTP |
-Related structure data
Related structure data | 21667MC 6wh7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 41130.918 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penaeus monodon metallodensovirus / Gene: ORF4 / Plasmid: pFastBac1-HM / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) #2: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Penaeus monodon metallodensovirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Penaeus monodon metallodensovirus |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 / Plasmid: pFastBac1-HM |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Penaeus monodon |
Virus shell | Triangulation number (T number): 1 |
Buffer solution | pH: 8.2 Details: 20 mM HEPES, 20 mM MES, 20 mM sodium acetate, 0.15 M NaCl, 3.7 mM CaCl2 |
Buffer component | Name: Universal buffer |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 75 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10-2155_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 12873 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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