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- EMDB-2401: Electron cryo-microscopy of emptied cricket parvovirus AdDNV -

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Basic information

Entry
Database: EMDB / ID: EMD-2401
TitleElectron cryo-microscopy of emptied cricket parvovirus AdDNV
Map dataReconstruction of emptied cricket parvovirus
Sample
  • Sample: Cricket parvovirus AdDNV
  • Virus: Parvovirus
Keywordsinvertebrate parvovirus / emptied particle / parvovirus infection process
Biological speciesParvovirus
Methodsingle particle reconstruction / cryo EM
AuthorsGeng M / XinZheng Z / Pavel P / Qian Y / Peter T / Michael GR
CitationJournal: J Virol / Year: 2013
Title: The structure and host entry of an invertebrate parvovirus.
Authors: Geng Meng / Xinzheng Zhang / Pavel Plevka / Qian Yu / Peter Tijssen / Michael G Rossmann /
Abstract: The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate ...The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.
History
DepositionJun 24, 2013-
Header (metadata) releaseJul 24, 2013-
Map releaseJul 2, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2401.png

Downloads & links

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Map

FileDownload / File: emd_2401.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of emptied cricket parvovirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.5 / Movie #1: 2.5
Minimum - Maximum-6.82489014 - 10.07446575
Average (Standard dev.)0.22455701 (±1.00000012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 328.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z328.800328.800328.800
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-6.82510.0740.225

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Supplemental data

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Sample components

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Entire : Cricket parvovirus AdDNV

EntireName: Cricket parvovirus AdDNV
Components
  • Sample: Cricket parvovirus AdDNV
  • Virus: Parvovirus

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Supramolecule #1000: Cricket parvovirus AdDNV

SupramoleculeName: Cricket parvovirus AdDNV / type: sample / ID: 1000 / Number unique components: 60

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Supramolecule #1: Parvovirus

SupramoleculeName: Parvovirus / type: virus / ID: 1 / NCBI-ID: 10781 / Sci species name: Parvovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Acheta domesticus (house cricket) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Name: vp4

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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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJan 5, 2013
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Number images used: 17000

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