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The structure of JC polyomavirus (pH 7.4)

by single particle (icosahedral) reconstruction, at 19 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 43, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 43, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5183
TitleThe structure of JC polyomavirus (pH 7.4)
MapCryo-EM reconstruction of JC polyomavirus (pH 7.4)
SampleJC polyomavirus in buffer A (pH 7.4)
KeywordsJC, JCV, polyomavirus
AuthorsShen PS, Enderlein D, Nelson C, Carter WS, Kawano M, Xing L, Swenson RD, Olson NH, Baker TS, Cheng RH, Atwood WJ, Johne R, Belnap DM
DateDeposition: 2010-04-12, Header release: 2010-12-08, Map release: 2011-01-19, Last update: 2011-09-23
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 43, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 43, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleVirology, Vol. 411, Issue 1, Page 142-52, Year 2011
TitleThe structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.
AuthorsPeter S Shen, Dirk Enderlein, Christian D S Nelson, Weston S Carter, Masaaki Kawano, Li Xing, Robert D Swenson, Norman H Olson, Timothy S Baker, R Holland Cheng, Walter J Atwood, Reimar Johne, David M Belnap
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
KeywordsAnimals, Capsid (ultrastructure), Capsid Proteins (metabolism), Cryoelectron Microscopy, Macromolecular Substances (ultrastructure), Melopsittacus (virology), Polyomavirus (isolation & purification)
LinksDOI: 10.1016/j.virol.2010.12.005, PubMed: 21239031, PMC: PMC3057058
Map
Fileemd_5183.map.gz ( map file in CCP4 format, 193091 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
367 pix
1.62 A/pix
= 597.78 A
367 pix
1.62 A/pix
= 597.78 A
367 pix
1.62 A/pix
= 597.78 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:43 (by author), 43 (movie #1):
Minimum - Maximum: -72.7188 - 139.522
Average (Standard dev.): 10.425 (32.6366)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions367367367
Origin-183-183-183
Limit183183183
Spacing367367367
Unit CellA= B= C: 597.78 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.62 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.621.621.62
M x/y/z369369369
origin x/y/z0.0000.0000.000
length x/y/z597.780597.780597.780
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-183-183-183
NC/NR/NS367367367
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-72.719139.52210.425
Annotation DetailsCryo-EM reconstruction of JC polyomavirus (pH 7.4)
Supplement
Images
Images
Sample
NameJC polyomavirus in buffer A (pH 7.4)
Number of Components1
Oligomeric Statevirions
Component #1: virus - JCV
Scientific nameJC polyomavirus
Common NameJCV
DetailsCryo-EM of JC polyomavirus over holey carbon grids
Scientific Name of SpeciesJC polyomavirus
Common Name of SpeciesJCV
NCBI taxonomy10632
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: VERTEBRATES
ShellID: 1 , Diameter: 5000 A, Name Element: VP1 , T Number: 7
Experiment
Sample Preparation
Specimen Conc1.5 mg/ml
Specimen Support Details200 mesh copper grid (holey carbon)
Specimen Stateparticle
BufferDetails: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2
pH: 7.4
Vitrification
Method3 second blot before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere
Humidity100
InstrumentFEI VITROBOT
Temperature89 Kelvin
Imaging
MicroscopeFEI TECNAI F30
Date23-APR-2007
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 39000, Calibrated: 39000
Astigmatismastigmatism was corrected at 59,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus500 nm - 4900 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Temperature90 K ( 88 - 95 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images50
Sampling Size6.35
Quant Bit Number16
DetailsMicrographs digitized in positive contrast mode.
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmcommon lines
SoftwarePFT2 and EM3DR2
CTF Correctioneach micrograph
Resolution By Author19 A
Resolution MethodFSC 0.333
Single Particle
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5183.xml (7.8 KB)
Map dataemd_5183.map.gz (91.1 MB)
Imagesemd_5183_1.jpg (36.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5183
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.6 MB
Session file for UCSF-Chimera, 26.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.1 KB