|Entry||Database: EMDB / ID: 9363|
|Title||Structure of M. spretus Endogenous Virus Element (EVE) Virus-like particle (VLP)|
|Map data||Icosahedrally averaged density map of M. spretus Endogenous Virus Element (EVE) Virus-like particle (VLP)|
virus / Mus Spretus Endogenous Viral Element
|Source||Parvoviridae (virus) / Mus spretus (western wild mouse)|
|Method||single particle reconstruction / cryo EM / 3.89 Å resolution|
|Authors||Callaway HM / Subramanian S|
|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 Urbina / Karen Barnard / Robert Dick / Carol M Bator / Susan L Hafentein / 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 could be 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 N-acetyl neuraminic acid, and entered murine L cells. The 3.89Å structure of the 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 EVEs incorporated into the genomes of different animals represent remnants of the DNA sequences 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.
|Validation Report||PDB-ID: 6nf9|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 19, 2018 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9363.map.gz (map file in CCP4 format, 202613 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.08 Å|
CCP4 map header:
|Entire||Name: Parvoviridae / Number of components: 2|
-Component #1: virus, Parvoviridae
|Virus||Name: Parvoviridae / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER|
|Species||Species: Parvoviridae (virus) / Strain: Mus spretus endogenous viral element|
|Source (engineered)||Expression System: Trichoplusia ni (cabbage looper)|
|Source (natural)||Host Species: Mus spretus (western wild mouse)|
-Component #2: protein, Mus Spretus Endogenous Viral Element
|Protein||Name: Mus Spretus Endogenous Viral Element / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 63.76059 kDa|
|Source||Species: Mus spretus (western wild mouse)|
|Source (engineered)||Expression System: Trichoplusia ni (cabbage looper)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: Phosphate buffered saline pH 7.4 / pH: 7.4|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: DARK FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON III (4k x 4k)|
|Image acquisition||Number of digital images: 2082|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 6342|
|3D reconstruction||Software: RELION / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF|
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