+Open data
-Basic information
Entry | Database: PDB / ID: 6shl | |||||||||
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Title | Structure of a marine algae virus of the order Picornavirales | |||||||||
Components |
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Keywords | VIRUS / Picornavirales / Marnaviridae / icosahedral virus / algae virus / jelly roll | |||||||||
Function / homology | Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Predicted structural protein / Predicted structural protein Function and homology information | |||||||||
Biological species | Chaetoceros tenuissimus RNA virus type-II | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Munke, A. / Tomaru, Y. / Kimura, K. / Okamoto, K. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: J Virol / Year: 2020 Title: Capsid Structure of a Marine Algal Virus of the Order . Authors: Anna Munke / Kei Kimura / Yuji Tomaru / Kenta Okamoto / Abstract: The order includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as ...The order includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the ancestor in some respects. Herein, we present the capsid structure of RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first alga virus belonging to the family of the order A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, revealed that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of viruses. The above-mentioned and other critical structural features provide new insights on three long-standing theories about : (i) the canyon hypothesis, (ii) the primordial VP2 domain swap, and (iii) the hypothesis that alga viruses could share characteristics with the ancestor. Identifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes and thus still share some characteristics with the ancestor. This article describes the first atomic capsid structure of an alga , CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of viruses. | |||||||||
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 | 6shl.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6shl.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 6shl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6shl_validation.pdf.gz | 960.4 KB | Display | wwPDB validaton report |
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Full document | 6shl_full_validation.pdf.gz | 964.8 KB | Display | |
Data in XML | 6shl_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 6shl_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/6shl ftp://data.pdbj.org/pub/pdb/validation_reports/sh/6shl | HTTPS FTP |
-Related structure data
Related structure data | 10200MC 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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-Components
#1: Protein | Mass: 29740.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VJB4 |
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#2: Protein | Mass: 25911.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VJB4 |
#3: Protein | Mass: 28508.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VJB4 |
#4: Protein | Mass: 5406.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VMZ2, UniProt: A0A0B6VJB4*PLUS |
-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: Chaetoceros tenuissimus RNA virus type-II / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Chaetoceros tenuissimus RNA virus type-II |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Chaetoceros tenuissimus |
Virus shell | Name: Capsid / Triangulation number (T number): 3 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 / Nominal magnification: 140000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 29 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2592 |
Image scans | Movie frames/image: 32 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9920 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8315 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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