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Poliovirus 135S particle and P1 Fab complex at 12-angs. resolution

by single particle (icosahedral) reconstruction, at 12 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 8.6, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 8.6, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5280
TitlePoliovirus 135S particle and P1 Fab complex at 12-angs. resolution
MapThis is a map of poliovirus 135S and P1 Fab complex at 12-ang resolution
SamplePoliovirus 135S particle and P1(monospecific antibody) Fab complex
Keywordspicornavirus, viral cell entry, viral uncoating, virus-antibody complex, virus-Fab complex, virus disassembly, virus uncoating, virus conformational transitions, monospecific antibody
AuthorsLin J, Cheng N, Chow M, Filman DJ, Steven AC, Hogle JM, Belnap DM
DateDeposition: 2011-05-02, Header release: 2011-05-05, Map release: 2012-03-08, Last update: 2012-10-03
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 8.6, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 8.6, Image 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
ArticleJ. Virol., Vol. 85, Issue 19, Page 9974-83, Year 2011
TitleAn externalized polypeptide partitions between two distinct sites on genome-released poliovirus particles.
AuthorsJun Lin, Naiqian Cheng, Marie Chow, David J Filman, Alasdair C Steven, James M Hogle, David M Belnap
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
KeywordsCapsid Proteins (chemistry), Cryoelectron Microscopy, HeLa Cells, Humans, Imaging, Three-Dimensional, Models, Molecular, Poliovirus (physiology), RNA, Viral (metabolism), VP1 protein, Poliovirus, Virion (chemistry), Virus Uncoating
LinksDOI: 10.1128/JVI.05013-11, PubMed: 21775460, PMC: PMC3196412
Map
Fileemd_5280.map.gz ( map file in CCP4 format, 74354 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
267 pix
1.83 A/pix
= 488.61 A
267 pix
1.83 A/pix
= 488.61 A
267 pix
1.83 A/pix
= 488.61 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:8.6 (by author), 8.6 (movie #1):
Minimum - Maximum: -31.67783546 - 96.89107513
Average (Standard dev.): 5.0518713 (17.71579361)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions267267267
Origin-133-133-133
Limit133133133
Spacing267267267
Unit CellA= B= C: 488.61002 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.83 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.831.831.83
M x/y/z267267267
origin x/y/z0.0000.0000.000
length x/y/z488.610488.610488.610
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-133-133-133
NC/NR/NS267267267
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-31.67896.8915.052
Annotation DetailsThis is a map of poliovirus 135S and P1 Fab complex at 12-ang resolution
Supplement
Images
Images
Sample
NamePoliovirus 135S particle and P1(monospecific antibody) Fab complex
Number of Components2
Oligomeric State135S particle icosahedral with Fab
Component #1: virus - poliovirus 135S
Scientific nameHuman poliovirus 1 Mahoney
Common Namepoliovirus 135S
Detailsnative virus 160S is converted by heat-treatment to 135S
Scientific Name of SpeciesHuman poliovirus 1 Mahoney
Common Name of Speciespoliovirus 135S
NCBI taxonomy12081
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: VERTEBRATES
ShellID: 1 , Diameter: 340 A, T Number: 1
Experiment
Sample Preparation
Specimen Stateparticle
BufferDetails: 20 mM Tris, 2 mM CaCl2
pH: 7.5
Vitrification
MethodBlotted manually before plunging
Cryogen NameETHANE
DetailsVitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Date15-JUL-1999
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 38000, Calibrated: 37752
AstigmatismBsoft
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus810 nm - 2240 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images14
Sampling Size7
Quant Bit Number8
DetailsDefocal pairs were used.
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmFourier Bessel
SoftwareEM3DR2
CTF CorrectionCTF and decay correction of each particle
DetailsReconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Resolution By Author12 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections10160
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5280.xml (7.7 KB)
Map dataemd_5280.map.gz (34.7 MB)
Imagesemd_5280_1.jpg (2.1 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5280
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 25.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 4 MB
Session file for UCSF-Chimera, 26.3 KB