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Yorodumi- PDB-6nf9: Structure of M. spretus Endogenous Virus Element (EVE) Virus-like... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nf9 | ||||||||||||
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Title | Structure of M. spretus Endogenous Virus Element (EVE) Virus-like particle (VLP) | ||||||||||||
Components | Mus Spretus Endogenous Viral Element | ||||||||||||
Keywords | VIRUS LIKE PARTICLE / Mus spretus / VLP / EVE | ||||||||||||
Function / homology | Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Beta Complex / Mainly Beta Function and homology information | ||||||||||||
Biological species | Mus spretus (western wild mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å | ||||||||||||
Authors | Callaway, H.M. / Subramanian, S. | ||||||||||||
Funding support | United States, United Kingdom, 3items
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Citation | Journal: J Virol / Year: 2019 Title: Examination and Reconstruction of Three Ancient Endogenous Parvovirus Capsid Protein Gene Remnants Found in Rodent Genomes. Authors: Heather M Callaway / Suriyasri Subramanian / Christian A Urbina / Karen N Barnard / Robert A Dick / Carol M Bator / Susan L Hafenstein / Robert J Gifford / Colin R Parrish / Abstract: Parvovirus-derived endogenous viral elements (EVEs) have been found in the genomes of many different animal species, resulting from integration events that may have occurred from more than 50 million ...Parvovirus-derived endogenous viral elements (EVEs) have been found in the genomes of many different animal species, resulting from integration events that may have occurred from more than 50 million years ago to much more recently. Here, we further investigate the properties of autonomous parvovirus EVEs and describe their relationships to contemporary viruses. While we did not find any intact capsid protein open reading frames in the integrated viral sequences, we examined three EVEs that were repaired to form full-length sequences with relatively few changes. These sequences were found in the genomes of (brown rat), (Algerian mouse), and (wood mouse). The sequence was not present in the genomes of the closely related species , , , and , indicating that it was less than 2 million years old, and the and sequences were not found in the published genomes of other mouse species, also indicating relatively recent insertions. The VP2 sequence assembled into capsids, which had high thermal stability, bound the sialic acid -acetylneuraminic acid, and entered murine L cells. The 3.89-Å structure of the virus-like particles (VLPs), determined using cryo-electron microscopy, showed similarities to rodent and porcine parvovirus capsids. The repaired VP2 sequences from and did not assemble as first prepared, but chimeras combining capsid surface loops from with canine parvovirus assembled, allowing some of that capsid's structures and functions to be examined. Parvovirus endogenous viral elements (EVEs) that have been incorporated into the genomes of different animals represent remnants of the DNA sequences of ancient viruses that infected the ancestors of those animals millions of years ago, but we know little about their properties or how they differ from currently circulating parvoviruses. By expressing the capsid proteins of different parvovirus EVEs that were found integrated into the genomes of three different rodents, we can examine their structures and functions. A VP2 (major capsid protein) EVE sequence from a mouse genome assembled into capsids that had a similar structure and biophysical properties to extant parvoviruses and also bound sialic acids and entered rodent cells. Chimeras formed from combinations of canine parvovirus and portions of the parvovirus sequences from the brown rat genome allowed us to examine the structures and functions of the surface loops of that EVE capsid. | ||||||||||||
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 | 6nf9.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nf9.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nf9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6nf9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6nf9_validation.xml.gz | 29 KB | Display | |
Data in CIF | 6nf9_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/6nf9 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/6nf9 | HTTPS FTP |
-Related structure data
Related structure data | 9363MC 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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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 63760.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus spretus (western wild mouse) / Production host: Trichoplusia ni (cabbage looper) |
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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: Parvoviridae / Type: VIRUS / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Source (natural) | Organism: Parvoviridae (virus) / Strain: Mus spretus endogenous viral element | |||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | |||||||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||
Natural host | Organism: Mus spretus | |||||||||||||||||||||||||
Virus shell | Diameter: 250 nm / Triangulation number (T number): 1 | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: Phosphate buffered saline pH 7.4 | |||||||||||||||||||||||||
Buffer component |
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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: FLOOD BEAM |
Electron lens | Mode: DARK FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2082 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
Particle selection | Num. of particles selected: 47 | |||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||
3D reconstruction | Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6342 / Num. of class averages: 1 / Symmetry type: POINT |