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- EMDB-48927: The Turkey Parvovirus Capsid structure -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48927
TitleThe Turkey Parvovirus Capsid structure
Map data
Sample
  • Virus: Turkey parvovirus 260
    • Protein or peptide: VP2
  • Ligand: MAGNESIUM ION
KeywordsCapsid / Aveparvovirus / Turkey Parvovirus / cryo-EM / TuPV / VIRUS
Function / homologyParvovirus 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 / VP2
Function and homology information
Biological speciesTurkey parvovirus 260
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsHsi J / Mietzsch M / McKenna R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
National Science Foundation (NSF, United States)DGE-2236414 United States
CitationJournal: To be published
Title: Birds of a Feather Flock Together: Structural Characterization of Red-Crowned Crane and Turkey Aveparvoviruses
Authors: Hsi J / Mietzsch M / Patney M / Chen S / Sawh-Gopal A / Chipman P / McKenna R
History
DepositionFeb 4, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48927.png

Downloads & links

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Map

FileDownload / File: emd_48927.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.72 Å/pix.
x 500 pix.
= 360. Å		0.72 Å/pix.
x 500 pix.
= 360. Å		0.72 Å/pix.
x 500 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-7.913453 - 16.039439999999999
Average (Standard dev.)0.000000000103233 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48927_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_48927_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 : Turkey parvovirus 260

EntireName: Turkey parvovirus 260
Components
  • Virus: Turkey parvovirus 260
    • Protein or peptide: VP2
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Turkey parvovirus 260

SupramoleculeName: Turkey parvovirus 260 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 740934 / Sci species name: Turkey parvovirus 260 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Turkey parvovirus 260
Molecular weightTheoretical: 60.426852 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADENEPDQS GIPMELSDGP GTVGGGGGGG IGHSTGNWNC DTIWAENTCK TYASRHCVCL MRDMDQYKAI GNANGQHGLD TENQTQYFG FSTPWNYIDF NQYSVHFSPR DWQQLVNNYS RWRPRAVHVK IFNLQVIQKT VTDSGTQYSN DLTGTIQIFA D QEGRYPRL ...String:
MADENEPDQS GIPMELSDGP GTVGGGGGGG IGHSTGNWNC DTIWAENTCK TYASRHCVCL MRDMDQYKAI GNANGQHGLD TENQTQYFG FSTPWNYIDF NQYSVHFSPR DWQQLVNNYS RWRPRAVHVK IFNLQVIQKT VTDSGTQYSN DLTGTIQIFA D QEGRYPRL LYPNQTTLMG PFPSNIYYLP QYAYMTSMFN SGGPTVSSWW GFPTRESAFY CLDESPSQML RTGNEWETTF VF PSSTQWC NNKISTVSIT QRQNPLYDTW NVNGRGDDAK RGNFCTWRSP WYPGPYIYLT DTSAASQRLE NLANVAVGPD GMP LAPGMP QYRSESDKDE YLHTFWVPKK VKMNEGDIRN AQIDVSTATK VQVDTSTLYN TCPRSGYMST VSQGGAPAPI VWSG CVPGM IWDNRPATYF DPIWQQFPET DEQFKIISQL GGIPVKESPG HIFVKVTPKP TGAANGLIDE YCTFTCTVEI EWELE PLNT HRWNMRSMIS YETTDAKAGR QIVDENGQYQ VNVNSADITR LYMTKRAPRT N

UniProtKB: VP2

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 120 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.99 µm / Nominal defocus min: 0.9500000000000001 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35131
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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