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- EMDB-9363: Structure of M. spretus Endogenous Virus Element (EVE) Virus-like... -

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Basic information

Entry
Database: EMDB / ID: EMD-9363
TitleStructure of M. spretus Endogenous Virus Element (EVE) Virus-like particle (VLP)
Map dataIcosahedrally averaged density map of M. spretus Endogenous Virus Element (EVE) Virus-like particle (VLP)
Sample
  • Virus: Parvoviridae (virus)
    • Protein or peptide: Mus Spretus Endogenous Viral Element
KeywordsMus spretus / VLP / EVE / VIRUS LIKE PARTICLE
Biological speciesMus spretus (western wild mouse) / Parvoviridae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsCallaway HM / Subramanian S
Funding support United States, United Kingdom, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI092571 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM080533 United States
Medical Research Council (MRC, United Kingdom)MC_UU_12014/10 United Kingdom
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 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
DepositionDec 19, 2018-
Header (metadata) releaseJan 23, 2019-
Map releaseJan 23, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nf9
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nf9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9363.png

Downloads & links

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Map

FileDownload / File: emd_9363.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedrally averaged density map of M. spretus Endogenous Virus Element (EVE) Virus-like particle (VLP)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 370 pix.
= 399.6 Å		1.08 Å/pix.
x 370 pix.
= 399.6 Å		1.08 Å/pix.
x 370 pix.
= 399.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.153098 - 0.2875262
Average (Standard dev.)0.0012813112 (±0.018605033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-185-185-185
Dimensions370370370
Spacing370370370
CellA=B=C: 399.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z399.600399.600399.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-185-185-185
NC/NR/NS370370370
D min/max/mean-0.1530.2880.001

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Supplemental data

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Sample components

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Entire : Parvoviridae

EntireName: Parvoviridae (virus)
Components
  • Virus: Parvoviridae (virus)
    • Protein or peptide: Mus Spretus Endogenous Viral Element

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Supramolecule #1: Parvoviridae

SupramoleculeName: Parvoviridae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10780 / Sci species name: Parvoviridae / Sci species strain: Mus spretus endogenous viral element / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Mus spretus (western wild mouse)
Virus shellShell ID: 1 / Diameter: 250.0 Å / T number (triangulation number): 1

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Macromolecule #1: Mus Spretus Endogenous Viral Element

MacromoleculeName: Mus Spretus Endogenous Viral Element / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus spretus (western wild mouse)
Molecular weightTheoretical: 63.76059 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSHDAQPNEQ PNTGIELATG GNGSGSSGGG GRGAGGVGVS TGSFNNQTEF HYLGDGLVQI TAHASRLVHL NMPEHESYRR INVLNSEAG VAGQMVQDDA HSQMVTPWSL VDANAWGVWF NPGDWQLITN NMTELNLVSF EQEIFNVVLK TITESATTPP T KIYNNDLT ...String:
MSHDAQPNEQ PNTGIELATG GNGSGSSGGG GRGAGGVGVS TGSFNNQTEF HYLGDGLVQI TAHASRLVHL NMPEHESYRR INVLNSEAG VAGQMVQDDA HSQMVTPWSL VDANAWGVWF NPGDWQLITN NMTELNLVSF EQEIFNVVLK TITESATTPP T KIYNNDLT ASLMVALDTN NTLPYTPAAP RSETLGFYPW LPTKPTHYRY YMTCTRNLTP PTHTGQAGTI TNTISAPTHS DV MFYTIEN AVPIHLLRTG DEFSTGTYYF DTKPLKMTHS WQTNRSLGLP PKLATEPTTE GQQHTGTLKA ATDREGIHQT INN SYTEAT ALRPAQVGYN TPYMNFEYSD GGPFLTPIVP VYDTQYNADE PNGAYRITMG YQHGQITTAT ELGRYTLNPI SKGG RAPNQ EFNQSSPLQM ENTLNGTLLP TDPIGGKTDI HFTNTLNTYG PLTALNNTPP IYPNGQIWDK ELDADLKPRL HVTAP FVCK NNPPGQLFVK IAPNLTDDFN ADSPQQPRII TYSNFWWKGT LTFTARMRSS NMWNPIHQHT TTNDNIVNYM PSNIGG MRL YPEIPQLIPR KLY

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
1.7 mMKClpotassium chloride
10.0 mMNa2HPO4sodium phosphate dibasic
1.8 mMKH2PO4potassium phosphate monobasic

Details: Phosphate buffered saline pH 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 2082 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 47
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 6342
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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