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- EMDB-1467: Human Parvovirus B19 (empty wildtype particle) -

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Basic information

Entry
Database: EMDB / ID: EMD-1467
TitleHuman Parvovirus B19 (empty wildtype particle)
Map dataHuman Parvovirus B19 (eB19, empty wildtype particle)
Sample
  • Sample: Human Parvovirus B19 (empty wildtype particle)
  • Virus: Human parvovirus B19
Keywordsicosahedral / empty viral particle / B19
Biological speciesHuman parvovirus B19
Methodsingle particle reconstruction / cryo EM / Resolution: 11.3 Å
AuthorsKaufmann B / Chipman PR / Modrow S / Rossmann MG
CitationJournal: J Virol / Year: 2008
Title: Visualization of the externalized VP2 N termini of infectious human parvovirus B19.
Authors: Bärbel Kaufmann / Paul R Chipman / Victor A Kostyuchenko / Susanne Modrow / Michael G Rossmann /
Abstract: The structures of infectious human parvovirus B19 and empty wild-type particles were determined by cryoelectron microscopy (cryoEM) to 7.5-A and 11.3-A resolution, respectively, assuming icosahedral ...The structures of infectious human parvovirus B19 and empty wild-type particles were determined by cryoelectron microscopy (cryoEM) to 7.5-A and 11.3-A resolution, respectively, assuming icosahedral symmetry. Both of these, DNA filled and empty, wild-type particles contain a few copies of the minor capsid protein VP1. Comparison of wild-type B19 with the crystal structure and cryoEM reconstruction of recombinant B19 particles consisting of only the major capsid protein VP2 showed structural differences in the vicinity of the icosahedral fivefold axes. Although the unique N-terminal region of VP1 could not be visualized in the icosahedrally averaged maps, the N terminus of VP2 was shown to be exposed on the viral surface adjacent to the fivefold beta-cylinder. The conserved glycine-rich region is positioned between two neighboring, fivefold-symmetrically related VP subunits and not in the fivefold channel as observed for other parvoviruses.
History
DepositionFeb 5, 2008-
Header (metadata) releaseFeb 7, 2008-
Map releaseMar 31, 2009-
UpdateMar 31, 2009-
Current statusMar 31, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 18
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 18
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1467.gif

Downloads & links

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Map

FileDownload / File: emd_1467.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Parvovirus B19 (eB19, empty wildtype particle)
Voxel sizeX=Y=Z: 2.81649 Å
Density
Contour Level1: 11.0 / Movie #1: 18
Minimum - Maximum-10.31 - 34.561
Average (Standard dev.)2.24292 (±8.7631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-55-55-55
Dimensions111111111
Spacing111111111
CellA=B=C: 312.63 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.81648648648652.81648648648652.8164864864865
M x/y/z111111111
origin x/y/z0.0000.0000.000
length x/y/z312.630312.630312.630
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S213
start NC/NR/NS-55-55-55
NC/NR/NS111111111
D min/max/mean-10.31034.5612.243

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Supplemental data

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Sample components

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Entire : Human Parvovirus B19 (empty wildtype particle)

EntireName: Human Parvovirus B19 (empty wildtype particle)
Components
  • Sample: Human Parvovirus B19 (empty wildtype particle)
  • Virus: Human parvovirus B19

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Supramolecule #1000: Human Parvovirus B19 (empty wildtype particle)

SupramoleculeName: Human Parvovirus B19 (empty wildtype particle) / type: sample / ID: 1000
Details: icosahedral, empty viral particle, non-enveloped protein shell
Oligomeric state: 60 VP subunits form icosahedral protein shell
Number unique components: 1
Molecular weightTheoretical: 3.6 MDa

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Supramolecule #1: Human parvovirus B19

SupramoleculeName: Human parvovirus B19 / type: virus / ID: 1 / Name.synonym: Human Parvovirus B19
Details: empty wildtype particles purified from human plasma, no ssDNA genome encapsidated
NCBI-ID: 10798 / Sci species name: Human parvovirus B19 / Virus type: OTHER / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: Human Parvovirus B19
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 3.6 MDa
Virus shellShell ID: 1 / Diameter: 260 Å / T number (triangulation number): 1

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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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 25mM Tris-HCl
GridDetails: 400 mesh copper
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: guillotine-style plunge freezing device
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.66 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 45000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 98 K
Alignment procedureLegacy - Astigmatism: live FFT at 200K
Detailslow dose
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 31 / Average electron dose: 22 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMPFT, POR, P3DR
Details: final map includes data to 10.5 Ang resolution (fsc 0.3 cut-off), magnification of final map standardized to a map calculated from B19 VP2 VLP model coordinates (PDB accession no 1S58) ...Details: final map includes data to 10.5 Ang resolution (fsc 0.3 cut-off), magnification of final map standardized to a map calculated from B19 VP2 VLP model coordinates (PDB accession no 1S58) resulting in final pixel separation of 2.8165Ang
Number images used: 1959
Detailsmanual particle selection

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