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- EMDB-48926: The Red Crowned-Crane Parvovirus Capsid -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48926
TitleThe Red Crowned-Crane Parvovirus Capsid
Map data
Sample
  • Virus: Red-crowned crane parvovirus
    • Protein or peptide: Major capsid protein
  • Ligand: MAGNESIUM ION
KeywordsRCPV / Aveparvovirus / Parvovirus / capsid / VLP / cryo-EM / 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 / Major capsid protein
Function and homology information
Biological speciesRed-crowned crane parvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsHsi J / Mietzsch M / McKenna R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-2236414 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 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_48926.png

Downloads & links

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Map

FileDownload / File: emd_48926.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-7.105829 - 13.939101000000001
Average (Standard dev.)-0.000000001928945 (±0.99999994)
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: #2

Fileemd_48926_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48926_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 : Red-crowned crane parvovirus

EntireName: Red-crowned crane parvovirus
Components
  • Virus: Red-crowned crane parvovirus
    • Protein or peptide: Major capsid protein
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Red-crowned crane parvovirus

SupramoleculeName: Red-crowned crane parvovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2079601 / Sci species name: Red-crowned crane parvovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Red-crowned crane parvovirus
Molecular weightTheoretical: 58.906148 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAADSSADA AVPMSDSPSG GGGGGGGGGI GESTGNWTCN TVWGKNSIIT NASRHCVCLT RDLDMYKAIG NKDNGLVFGT ENKTAWVGW STPWNYIDYN QMCVHFSPRD WQRLINTASK WRPRSVHIKI FNIQVIQKTT VSDGTQYSND LTGTIQIFAD A QGRYPKLL ...String:
MAAADSSADA AVPMSDSPSG GGGGGGGGGI GESTGNWTCN TVWGKNSIIT NASRHCVCLT RDLDMYKAIG NKDNGLVFGT ENKTAWVGW STPWNYIDYN QMCVHFSPRD WQRLINTASK WRPRSVHIKI FNIQVIQKTT VSDGTQYSND LTGTIQIFAD A QGRYPKLL YPCQTTMMGP FPNHIYYLPQ YAYTTACDGP TSNQDINALL NTNSAFYCLD ESPSAMLRTG NEWSCHYTFD DD TGWVHNT RSTIPIFERA NPLYDTWQVD LRGNDALRGH FSSWRQPWLP GPVINMTDGT AAGANLNTMP GVDVGASYMG IVP GPPICR AENDKDEYLQ TFWTPKTIGQ NEGDVKNSQI NTSTAYKSQV PTGRLWEVNA RGQYKAASSQ GNVADQQWAG CIPG MIWDR RPATYFDPIW QEKPITDDSF MYVSQMGGCT VSGAPGHIFV KNTPKPTGTA NEYVDEYSTF TITVTMEWEY EPHSF SQWN NYKMISNNES SAQAYVGMCN ASGQYVLNHS AGQLPEMWIT KNLSRVN

UniProtKB: Major capsid protein

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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: 1.9000000000000001 µm / Nominal defocus min: 0.47000000000000003 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 405850
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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