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Open data
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Basic information
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Title | The capsid structure of Human Parvovirus 4 | |||||||||
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![]() | Parvovirus / Capsid / PARV4 / Tetraparvovirus / Pathogen / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Phospholipase 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
![]() | Mietzsch M / McKenna R | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 368.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 73.9 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 140.2 MB 140.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ep9MC ![]() 8ep2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.9077 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28522_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28522_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Human parvovirus 4
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Human parvovirus 4
Supramolecule | Name: 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 |
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Virus shell | Shell ID: 1 / T number (triangulation number): 1 |
-Macromolecule #1: Human Parvovirus 4
Macromolecule | Name: Human Parvovirus 4 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 61.690828 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 UniProtKB: ORF2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5248 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: ANGULAR RECONSTITUTION |