+Open data
-Basic information
Entry | Database: PDB / ID: 6v7b | ||||||
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Title | Cryo-EM reconstruction of Pyrobaculum filamentous virus 2 (PFV2) | ||||||
Components |
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Keywords | VIRUS / helical symmetry / archaeal pilus / STRUCTURAL PROTEIN | ||||||
Function / homology | DNA / DNA (> 10) / DNA (> 100) / Structural protein VP1 / Structural protein VP2 Function and homology information | ||||||
Biological species | Pyrobaculum filamentous virus 1 | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Wang, F. / Baquero, D.P. / Su, Z. / Prangishvili, D. / Krupovic, M. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Virus Evol / Year: 2020 Title: Structure of a filamentous virus uncovers familial ties within the archaeal virosphere. Authors: Fengbin Wang / Diana P Baquero / Zhangli Su / Tomasz Osinski / David Prangishvili / Edward H Egelman / Mart Krupovic / Abstract: Viruses infecting hyperthermophilic archaea represent one of the most enigmatic parts of the global virome, with viruses from different families showing no genomic relatedness to each other or to ...Viruses infecting hyperthermophilic archaea represent one of the most enigmatic parts of the global virome, with viruses from different families showing no genomic relatedness to each other or to viruses of bacteria and eukaryotes. Tristromaviruses, which build enveloped filamentous virions and infect hyperthermophilic neutrophiles of the order Thermoproteales, represent one such enigmatic virus families. They do not share genes with viruses from other families and have been believed to represent an evolutionarily independent virus lineage. A cryo-electron microscopic reconstruction of the tristromavirus Pyrobaculum filamentous virus 2 at 3.4 Å resolution shows that the virion is constructed from two paralogous major capsid proteins (MCP) which transform the linear dsDNA genome of the virus into A-form by tightly wrapping around it. Unexpectedly, the two MCP are homologous to the capsid proteins of other filamentous archaeal viruses, uncovering a deep evolutionary relationship within the archaeal virosphere. | ||||||
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 | 6v7b.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6v7b.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6v7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/6v7b ftp://data.pdbj.org/pub/pdb/validation_reports/v7/6v7b | HTTPS FTP |
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-Related structure data
Related structure data | 21094MC 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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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 23 / Rise per n subunits: 2.864 Å / Rotation per n subunits: 22.9482 °) |
-Components
#1: DNA chain | Mass: 99669.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1 | ||
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#2: DNA chain | Mass: 99660.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1 | ||
#3: Protein | Mass: 14986.418 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1 / References: UniProt: A0A140F3K6 #4: Protein | Mass: 15326.556 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1 / References: UniProt: A0A140F3K7 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Pyrobaculum filamentous virus 2 / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Pyrobaculum filamentous virus 1 |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 90 % |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 2 sec. / Electron dose: 44 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 22.9482 ° / Axial rise/subunit: 2.864 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: OTHER / Num. of particles: 186576 / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Symmetry type: HELICAL |