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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
Function / homologyEmpty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Beta Complex / Mainly Beta
Function and homology information
Biological speciesMus spretus (western wild mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsCallaway, H.M. / Subramanian, S.
Funding support United States, United Kingdom, 3items
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, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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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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Assembly

Deposited unit
A: Mus Spretus Endogenous Viral Element


Theoretical massNumber of molelcules
Total (without water)63,7611
Polymers63,7611
Non-polymers00
Water00
1
A: Mus Spretus Endogenous Viral Element
x 60


Theoretical massNumber of molelcules
Total (without water)3,825,63560
Polymers3,825,63560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Mus Spretus Endogenous Viral Element
x 5


  • icosahedral pentamer
  • 319 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)318,8035
Polymers318,8035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers382,5646
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Mus Spretus Endogenous Viral Element


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Parvoviridae / Type: VIRUS / Entity ID: all / 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 / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Mus spretus
Virus shellDiameter: 250 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: Phosphate buffered saline 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
MicroscopyModel: 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) / Num. 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 selectionNum. of particles selected: 47
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6342 / Num. of class averages: 1 / Symmetry type: POINT

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