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- EMDB-28522: The capsid structure of Human Parvovirus 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-28522
TitleThe capsid structure of Human Parvovirus 4
Map data
Sample
  • Virus: Human parvovirus 4
    • Protein or peptide: Human Parvovirus 4Parvoviridae
Function / homologyPhospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / ORF2
Function and homology information
Biological speciesHuman parvovirus 4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsMietzsch M / McKenna R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2022
Title: Capsid Structure of Aleutian Mink Disease Virus and Human Parvovirus 4: New Faces in the Parvovirus Family Portrait.
Authors: Renuk Lakshmanan / Mario Mietzsch / Alberto Jimenez Ybargollin / Paul Chipman / Xiaofeng Fu / Jianming Qiu / Maria Söderlund-Venermo / Robert McKenna /
Abstract: Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. ...Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. Aleutian mink disease virus (AMDV), a pathogen in minks, and human parvovirus 4 (PARV4), infecting humans, are parvoviruses belonging to the genera and , respectively. While Aleutian mink disease caused by AMDV is a major threat to mink farming, no clear clinical manifestations have been established following infection with PARV4 in humans. Here, the capsid structures of AMDV and PARV4 were determined via cryo-electron microscopy at 2.37 and 3.12 Å resolutions, respectively. Despite low amino acid sequence identities (10-30%) both viruses share the icosahedral nature of parvovirus capsids, with 60 viral proteins (VPs) assembling the capsid via two-, three-, and five-fold symmetry VP-related interactions, but display major structural variabilities in the surface loops when the capsid structures are superposed onto other parvoviruses. The capsid structures of AMDV and PARV4 will add to current knowledge of the structural platform for parvoviruses and permit future functional annotation of these viruses, which will help in understanding their infection mechanisms at a molecular level for the development of diagnostics and therapeutics.
History
DepositionOct 5, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28522.png

Downloads & links

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Map

FileDownload / File: emd_28522.map.gz / Format: CCP4 / Size: 396.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.9077 Å
Density
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-9.839428 - 18.537859
Average (Standard dev.)5.779343e-10 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-235-235-235
Dimensions470470470
Spacing470470470
CellA=B=C: 426.619 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28522_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28522_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human parvovirus 4

EntireName: Human parvovirus 4
Components
  • Virus: Human parvovirus 4
    • Protein or peptide: Human Parvovirus 4Parvoviridae

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Supramolecule #1: Human parvovirus 4

SupramoleculeName: Human parvovirus 4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 289365 / Sci species name: Human parvovirus 4 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: Human Parvovirus 4

MacromoleculeName: Human Parvovirus 4 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Human parvovirus 4
Molecular weightTheoretical: 61.690828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSVEPAGGGG GVKVKAQWIG GTSFSDSVVI TSHTRTSMLA DRGGYVPVYK QGSHVDSSQP VMGMKTPYSY IDVNALSAHF TPRDFQQLL DEYDEIKPKS LTIAISAIVI KDVATNQTGT TVSDSASGGI TVFADDSYDY PYVLGHNQDT LPGHLPGENY V LPQYGYIT ...String:
MSVEPAGGGG GVKVKAQWIG GTSFSDSVVI TSHTRTSMLA DRGGYVPVYK QGSHVDSSQP VMGMKTPYSY IDVNALSAHF TPRDFQQLL DEYDEIKPKS LTIAISAIVI KDVATNQTGT TVSDSASGGI TVFADDSYDY PYVLGHNQDT LPGHLPGENY V LPQYGYIT RGREIDQQNS IVAISDHKTE LFFLEHHDAE CLGTGDHWSH HYEFPDDLPW RKLSTPNQTL YARHNPIPSS RL AIMTGVD NDGTAIWKRP EGMDVGRLPL NYVPGPALMM PTDTQIRNTT FRDPVAIGNP ATSDRYSVAP LVHQPWSVRT EEW LANKTD YAVHNYLGGV AYTRRKHEES YDKHEEDRDG RVTNPSRVVQ IDGDLAAPHV GHTFFVPGHT RVTSGGTDTV YSPK LYQEP VFPLFPGAVW NPNPLSYDCQ IWTKIPNTEC HFFAQYPLLG GWGVLTPPPM IFVKLRSQPG PPSPGAHTVP QSNLN QYAI FHLHYSMQFL VKRRKRSRRH NPEKPAPFPT TDSGRMPFTL ANSLKDPNTP VYEVPSDQWI ARNYSHLL

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cisTEM
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5248

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