|Entry||Database: EMDB / ID: EMD-1467|
|Title||Human Parvovirus B19 (empty wildtype particle)|
|Sample||Human Parvovirus B19 (empty wildtype particle):|
|Keywords||icosahedral / empty viral particle / B19|
|Biological species||Human parvovirus B19 (Human Parvovirus B19)|
|Method||single particle reconstruction / cryo EM / Resolution: 11.3 Å|
|Authors||Kaufmann B / Chipman PR / Modrow S / Rossmann MG|
|Citation||Journal: 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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_1467.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.81649 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Human Parvovirus B19 (empty wildtype particle)
|Entire||Name: Human Parvovirus B19 (empty wildtype particle)|
Details: icosahedral, empty viral particle, non-enveloped protein shell
Number of components: 1
Oligomeric State: 60 VP subunits form icosahedral protein shell
|Mass||Theoretical: 3.6 MDa|
-Component #1: virus, Human parvovirus B19
|Virus||Name: Human parvovirus B19 / a.k.a: Human Parvovirus B19 / Class: OTHER|
Details: empty wildtype particles purified from human plasma, no ssDNA genome encapsidated
Empty: Yes / Enveloped: No / Isolate: SPECIES
|Mass||Theoretical: 3.6 MDa|
|Species||Species: Human parvovirus B19 (Human Parvovirus B19)|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1 mg/mL / Buffer solution: 25mM Tris-HCl / pH: 7.5|
|Support film||400 mesh copper|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE|
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.
Details: Vitrification instrument: guillotine-style plunge freezing device
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM300FEG/T / Details: low dose|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 45000 X (nominal), 47000 X (calibrated) / Astigmatism: live FFT at 200K / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1250 - 3660 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 31 / Scanner: ZEISS SCAI / Sampling size: 14 µm / Bit depth: 8|
|Processing||Method: single particle reconstruction / Details: manual particle selection / Number of projections: 1959 / Applied symmetry: I (正20面体型対称)|
|3D reconstruction||Algorithm: model-based approach using Fourier methods / Software: EMPFT, POR, P3DR / CTF correction: each particle|
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
Resolution: 11.3 Å / Resolution method: FSC 0.5
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