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Human Parvovirus B19 (empty wildtype particle)

by single particle (icosahedral) reconstruction, at 11.3 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 18, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 18, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1467
TitleHuman Parvovirus B19 (empty wildtype particle)
MapHuman Parvovirus B19 (eB19, empty wildtype particle)
SampleHuman Parvovirus B19 (empty wildtype particle)
Keywordsicosahedral, empty viral particle, B19
AuthorsKaufmann B, Chipman PR, Modrow S, Rossmann MG
DateDeposition: 2008-02-05, Header release: 2008-02-07, Map release: 2009-03-31, Last update: 2009-03-31
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 18, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 18, Made by UCSF CHIMERA

Supplemental images

1467.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1466
Cite

EMDB-1468
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1739

EMDB-1907

EMDB-1468

EMDB-1326

EMDB-5415

EMDB-1837
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Virol., Vol. 82, Issue 15, Page 7306-12, Year 2008
TitleVisualization of the externalized VP2 N termini of infectious human parvovirus B19.
AuthorsBärbel Kaufmann, Paul R Chipman, Victor A Kostyuchenko, Susanne Modrow, Michael G Rossmann
Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.
KeywordsCapsid Proteins (chemistry), Cryoelectron Microscopy, Humans, Models, Molecular, Parvovirus B19, Human (chemistry), Protein Conformation, Virion (chemistry), capsid protein VP1, parvovirus B19, capsid protein VP2, parvovirus B19
LinksDOI: 10.1128/JVI.00512-08, PubMed: 18508892, PMC: PMC2493345
Map
FileEMD-1467.map ( map file in CCP4 format, 5472 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:11, 18 (movie #1):
Minimum - Maximum: -10.31 - 34.561
Average (Standard dev.): 2.24292 (8.7631)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions111111111
Origin-55-55-55
Limit555555
Spacing111111111
Unit CellA= B= C: 312.63 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.81649 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S213
start NC/NR/NS-55-55-55
NC/NR/NS111111111
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-10.31034.5612.243
Annotation DetailsHuman Parvovirus B19 (eB19, empty wildtype particle)
Supplement
Images
Images

1467.gif
Sample
NameHuman Parvovirus B19 (empty wildtype particle)
Number of Components1
Oligomeric State60 VP subunits form icosahedral protein shell
Theoretical Mass3.6MDa
Detailsicosahedral, empty viral particle, non-enveloped protein shell
Component #1: virus - Human Parvovirus B19
Scientific nameHuman parvovirus B19
Common NameHuman Parvovirus B19
Theoretical Mass3.6 MDa
Detailsempty wildtype particles purified from human plasma, no ssDNA genome encapsidated
Scientific Name of SpeciesHuman parvovirus B19
Common Name of SpeciesHuman Parvovirus B19
NCBI taxonomy10798
EmptyYes
EnvelopedNo
IsolateSPECIES
ClassOTHER
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: VERTEBRATES
ShellId: 1 , Diameter: 260 A, T Number: 1
Experiment
Sample Preparation
Specimen Conc1 mg/ml
Specimen Support Details400 mesh copper
Specimen Stateparticle
BufferDetails: 25mM Tris-HCl
pH: 7.5
Vitrification
MethodA 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.
Cryogen NameETHANE
DetailsVitrification instrument: guillotine-style plunge freezing device
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI/PHILIPS CM300FEG/T
Detailslow dose
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose22 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 45000, Calibrated: 47000
Astigmatismlive FFT at 200K
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1250 nm - 3660 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature98 K
Camera
DetectorKODAK SO163
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images31
Sampling Size14
Quant Bit Number8
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmmodel-based approach using Fourier methods
SoftwareEMPFT, POR, P3DR
CTF Correctioneach particle
Detailsfinal 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 By Author11.3 A
Resolution MethodFSC at 0.5 cut-off
Single Particle
Detailsmanual particle selection
Number of Projections1959
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-1467.xml (8.7 KB)
Map dataemd_1467.map.gz (2.5 MB)
Images1467.gif (101.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1467
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 19.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 19.5 KB