+Open data
-Basic information
Entry | Database: PDB / ID: 5oac | ||||||
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Title | FLiP major capsid protein | ||||||
Components | Major capsid protein | ||||||
Keywords | VIRUS / capsid / major capsid protein / virion | ||||||
Function / homology | Major capsid protein Function and homology information | ||||||
Biological species | unidentified phage (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | De Colibus, L. / Stuart, D.I. / Huiskonen, J.T. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Virus found in a boreal lake links ssDNA and dsDNA viruses. Authors: Elina Laanto / Sari Mäntynen / Luigi De Colibus / Jenni Marjakangas / Ashley Gillum / David I Stuart / Janne J Ravantti / Juha T Huiskonen / Lotta-Riina Sundberg / Abstract: Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because ...Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid. The 9,174-nt-long genome showed limited sequence similarity to other known viruses. The genetic data imply that this virus might use replication mechanisms similar to those found in other ssDNA replicons. However, the structure of the viral major capsid protein, elucidated at near-atomic resolution using cryo-electron microscopy, is strikingly similar to that observed in dsDNA viruses of the PRD1-adenovirus lineage, characterized by a major capsid protein bearing two β-barrels. The strong similarity between FLiP and another member of the structural lineage, bacteriophage PM2, extends to the capsid organization (pseudo = 21 ) despite the difference in the genetic material packaged and the lack of significant sequence similarity. | ||||||
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 | 5oac.cif.gz | 518.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oac.ent.gz | 445.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oac_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5oac_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5oac_validation.xml.gz | 105.1 KB | Display | |
Data in CIF | 5oac_validation.cif.gz | 154.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/5oac ftp://data.pdbj.org/pub/pdb/validation_reports/oa/5oac | HTTPS FTP |
-Related structure data
Related structure data | 3771MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 34533.934 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) unidentified phage (virus) / References: UniProt: A0A2D0TC94*PLUS |
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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: unidentified phage / Type: VIRUS Details: Flavobacterium infecting lipid-containing phage FLiP Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: unidentified phage (virus) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Flavobacterium / Strain: sp B330 |
Virus shell | Name: Capsid / Diameter: 550 nm / Triangulation number (T number): 25 |
Buffer solution | pH: 7.2 / Details: 20 mM PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/2 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Calibrated defocus min: 700 nm / Calibrated defocus max: 2500 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 22 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Sampling size: 5 µm / Movie frames/image: 22 / Used frames/image: 1-22 |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 934 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 84.31 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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