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- EMDB-48181: Goose Parvovirus Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-48181
TitleGoose Parvovirus Capsid
Map data
Sample
  • Virus: Goose parvovirus
    • Protein or peptide: VP1
KeywordsGPV / capsid / cryo-EM / parvovirus / gene therapy / vector / VIRUS LIKE PARTICLE
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 / VP1
Function and homology information
Biological speciesGoose parvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsJabbari K / Mietzsch 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: Microorganisms / Year: 2025
Title: The Structural, Biophysical, and Antigenic Characterization of the Goose Parvovirus Capsid.
Authors: Korosh Jabbari / Mario Mietzsch / Jane Hsi / Paul Chipman / Jianming Qiu / Robert McKenna /
Abstract: Goose parvovirus (GPV) is an etiological agent of Derzsy's disease, afflicting geese and Muscovy ducks worldwide. Its high mortality rate among goslings and ducklings causes large losses to the ...Goose parvovirus (GPV) is an etiological agent of Derzsy's disease, afflicting geese and Muscovy ducks worldwide. Its high mortality rate among goslings and ducklings causes large losses to the waterfowl industry. Toward molecular and structural characterization, virus-like particles (VLPs) of GPV were produced, and the capsid structure was determined by cryogenic electron microscopy (cryo-EM) at a resolution of 2.4 Å. The capsid exhibited structural features conserved among parvoviruses, including surface two-fold depressions, three-fold protrusions, and five-fold channels. A structural comparison of the GPV viral protein (VP) structure with other adeno-associated viruses (AAVs), including human AAV2, AAV5, and quail AAV (QAAV), revealed unique conformations of several surface-accessible variable regions (VRs). Furthermore, the GPV capsid was found to be thermally stable at physiological pH, but less so under lower pH conditions. As a member of the genus , GPV could also be bound by cross-reactive anti-AAV capsid antibodies that bind to the five-fold region of the viruses, as shown by native immuno-dot blot analysis. Finally, the GPV VP structure was compared to those of other bird dependoparvoviruses, which revealed that VR-III may be important for GPV and Muscovy duck parvovirus (MDPV) infection.
History
DepositionDec 5, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48181.png

Downloads & links

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Map

FileDownload / File: emd_48181.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)X (Row.)Y (Col.)
0.82 Å/pix.
x 500 pix.
= 411. Å		0.82 Å/pix.
x 500 pix.
= 411. Å		0.82 Å/pix.
x 500 pix.
= 411. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-8.236236 - 16.593575999999999
Average (Standard dev.)-0.000000000342541 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 411.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48181_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_48181_half_map_2.map
Projections & Slices
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Sample components

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Entire : Goose parvovirus

EntireName: Goose parvovirus
Components
  • Virus: Goose parvovirus
    • Protein or peptide: VP1

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Supramolecule #1: Goose parvovirus

SupramoleculeName: Goose parvovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 38251 / Sci species name: Goose parvovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Goose parvovirus
Molecular weightTheoretical: 81.551055 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTFLDSFEE WYETAAASWR NLKAGAPQPK PNQQSQSVSP DREPERKDNN RGFVLPGYKY LGPGNGLDKG PPVNKADSVA LEHDKAYDQ QLKAGDNPYI KFNHADQDFI DSLQDDQSFG GNLGKAVFQA KKRILEPFGL VEDPVNTAPA KKNTGKLTDH Y PVVKKPKL ...String:
MSTFLDSFEE WYETAAASWR NLKAGAPQPK PNQQSQSVSP DREPERKDNN RGFVLPGYKY LGPGNGLDKG PPVNKADSVA LEHDKAYDQ QLKAGDNPYI KFNHADQDFI DSLQDDQSFG GNLGKAVFQA KKRILEPFGL VEDPVNTAPA KKNTGKLTDH Y PVVKKPKL TEEVSAGGGS SAVQDGGATA EGTEPVAASE MAEGGGGAMG DSSGGADGVG NASGNWHCDS QWMGNTVITK TT RTWVLPS YNNHIYKAIT SGTSQDANVQ YAGYSTPWGY FDFNRFHCHF SPRDWQRLIN NHWGIRPKSL KFKIFNVQVK EVT TQDQTK TIANNLTSTI QVFTDDEHQL PYVLGSATEG TMPPFPSDVY ALPQYGYCTM HTNQNGARFN DRSAFYCLEY FPSQ MLRTG NNFEFTFDFE EVPFHSMFAH SQDLDRLMNP LVDQYLWNFN EVDSSRNAQF KKAVKGAYGT MGRNWLPGPK FLDQR VRAY TGGTDNYANW NIWSNGNKVN LKDRQYLLQP GPVSATYTEG EASSLPAQNI LGIAKDPYRS GSTTAGISDI MVTEEQ EVA PTNGVGWKPY GRTVTNEQNT TTAPTSSDLD VLGALPGMVW QNRDIYLQGP IWAKIPKTDG KFHPSPNLGG FGLHNPP PQ VFIKNTPVPA DPPVEYVHQK WNSYITQYST GQCTVEMVWE LRKENSKRWN PEIQFTSNFS NRTSIMFAPN ETGGYVED R LIGTRYLTQN L

UniProtKB: VP1

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.7 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15471
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION

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