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Poliovirus 80S particle and P1 Fab complex with Fab bound at propeller tip

by single particle (icosahedral) reconstruction, at 18 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 11.32, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 11.32, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5286
TitlePoliovirus 80S particle and P1 Fab complex with Fab bound at propeller tip
MapThis is a map of poliovirus 80S particle and P1 Fab complex with Fab bound at propeller tip only.
SamplePoliovirus 80S 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: 11.32, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 11.32, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Diagram

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EMDB-5283

EMDB-5123

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EMDB-5466
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-5286.map ( map file in CCP4 format, 76138 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (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:11.32 (by author), 11.32 (movie #1):
Minimum - Maximum: -32.75729752 - 90.33150482
Average (Standard dev.): 3.17764044 (16.40923500)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 267 267 267
Origin : -133 -133 -133
Limit : 133 133 133
Spacing : 267 267 267
Unit CellA = 488.61002 A , B = 488.61002 A , C = 488.61002 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 1.83 A , Y = 1.83 A , 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
NX/NY/NZ
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-32.75790.3323.178
Annotation DetailsThis is a map of poliovirus 80S particle and P1 Fab complex with Fab bound at propeller tip only.
Supplement
Sample
NamePoliovirus 80S particle and P1(monospecific antibody) Fab complex
Number of Components2
Oligomeric State80S particle icosahedral with Fab
Component #1: virus - poliovirus 80S
Scientific nameHuman poliovirus 1 Mahoney
Common Namepoliovirus 80S
Detailsnative virus 160S is converted by heat-treatment to 80S
Scientific Name of SpeciesHuman poliovirus 1 Mahoney (NCBI Taxonomy: 12081)
Common Name of Speciespoliovirus 80S
EmptyYes
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceHost Species: Homo sapiens (NCBI Taxonomy: 9606)
Host Category: VERTEBRATES
ShellDiameter: 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 X, Calibrated: 37752 X
AstigmatismBsoft
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus810 nm - 2240 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder ( GATAN LIQUID NITROGEN )
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images14
Sampling Size7 microns
Quant Bit Number8
DetailsDefocal pairs were used.
Processing
Methodsingle particle (icosahedral) reconstruction
3 D 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 Author18
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections1132
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5286.xml (7.8 KB)
Map dataemd_5286.map.gz (34.8 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5286
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4.2 MB
Session file for UCSF-Chimera, 25.8 KB