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- PDB-6nf9: Structure of M. spretus Endogenous Virus Element (EVE) Virus-like... -

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Entry
Database: PDB / ID: 6nf9
TitleStructure of M. spretus Endogenous Virus Element (EVE) Virus-like particle (VLP)
ComponentsMus Spretus Endogenous Viral Element
KeywordsVIRUS LIKE PARTICLE / Mus spretus / VLP / EVE
Specimen sourceMus spretus (western wild mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.89 Å resolution
AuthorsCallaway, H.M. / Subramanian, S.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Dec 19, 2018 / Release: Jan 23, 2019

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: Mus Spretus Endogenous Viral Element


Theoretical massNumber of molelcules
Total (without water)63,7611
Polyers63,7611
Non-polymers00
Water0
1
A: Mus Spretus Endogenous Viral Element
x 60


Theoretical massNumber of molelcules
Total (without water)3,825,63560
Polyers3,825,63560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Mus Spretus Endogenous Viral Element
x 5


  • icosahedral pentamer
  • 319 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)318,8035
Polyers318,8035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Mus Spretus Endogenous Viral Element
x 6


  • icosahedral 23 hexamer
  • 383 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)382,5646
Polyers382,5646
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide Mus Spretus Endogenous Viral Element


Mass: 63760.590 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus spretus (western wild mouse) / Production host: Trichoplusia ni (cabbage looper)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Parvoviridae / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Parvoviridae (virus) / Strain: Mus spretus endogenous viral element
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Mus spretus
Virus shellDiameter: 250 nm / Triangulation number (T number): 1
Buffer solutionDetails: Phosphate buffered saline pH 7.4 / pH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
1137 mMsodium chlorideNaCl1
21.7 mMpotassium chlorideKCl1
310 mMsodium phosphate dibasicNa2HPO41
41.8 mMpotassium phosphate monobasicKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Number of real images: 2082
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1RELION2.1particle selectionAutopicking
4GctfCTF correction
10RELION2.1initial Euler assignment
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 47
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6342 / Number of class averages: 1 / Symmetry type: POINT

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