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RNA-releasing poliovirus intermediates

by single particle (icosahedral) reconstruction, at 10 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 20.501312207, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 20.501312207, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3iyc, Surface level: 20.501312207, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3iyc, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5122
TitleRNA-releasing poliovirus intermediates
MapLATE early RNA-releasing 80S poliovirus
Sample80S poliovirus
KeywordsPicornavirus, poliovirus, intermediate, RNA-release, 80S
AuthorsLevy HC, Bostina M, Filman DJ, Hogle JM
DateDeposition: 2009-06-15, Header release: 2009-07-31, Map release: 2010-03-10, Last update: 2011-09-27
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 20.501312207, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 20.501312207, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3iyc, Surface level: 20.501312207, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3iyc, Image by Jmol

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

PDB-3iyc

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Fit: output model of fitting

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Article
Citation - Primary
ArticleJ. Virol., Vol. 84, Issue 9, Page 4426-41, Year 2010
TitleCatching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.
AuthorsHazel C Levy, Mihnea Bostina, David J Filman, James M Hogle
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
KeywordsCryoelectron Microscopy, HeLa Cells, Humans, Imaging, Three-Dimensional, Models, Molecular, Poliovirus (physiology), Protein Structure, Quaternary, RNA, Viral (metabolism), Virion (ultrastructure), Virus Internalization
LinksDOI: 10.1128/JVI.02393-09, PubMed: 20181687, PMC: PMC2863768
Map
Fileemd_5122.map.gz ( map file in CCP4 format, 31723 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
201 pix
2.3222985074627 A/pix
= 466.782 A
201 pix
2.3222985074627 A/pix
= 466.782 A
201 pix
2.3222985074627 A/pix
= 466.782 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2 (by author), 20.5013122 (movie #1):
Minimum - Maximum: -29.2078 - 68.0468
Average (Standard dev.): 1.89523 (8.2149)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions201201201
Origin-100-100-100
Limit100100100
Spacing201201201
Unit CellA= B= C: 466.782 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.3223 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.32229850746272.32229850746272.3222985074627
M x/y/z201201201
origin x/y/z0.0000.0000.000
length x/y/z466.782466.782466.782
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS201201201
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-29.20868.0471.895
Annotation DetailsLATE early RNA-releasing 80S poliovirus
Supplement
Images
Images
Sample
Name80S poliovirus
Number of Components1
Oligomeric State60 promoters arranged as a icosahedron
Theoretical Mass8.3MDa
Detailsnative virus heat-treated at 56 degrees C
Mass-estimation MethodSedimentation
Experimental Mass8.3MDa
Component #1: virus - poliovirus 1 mahoney
Scientific namepoliovirus 1 mahoney
Theoretical Mass8.3 MDa
Experimental Mass8.3 MDa
Detailsnative virus is converted by heat-treatment to 80S
Scientific Name of Speciespoliovirus 1 mahoney
Common Name of Speciespoliovirus 1 mahoney
EmptyYes
EnvelopedNo
IsolateSEROTYPE
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: VERTEBRATES
ShellID: 1 , Diameter: 290 A, Name Element: capsid , T Number: 1
Experiment
Sample Preparation
Stainingnot stained
Specimen Conc0.2 mg/ml
Specimen Support Details200 mesh copper grids
Specimen Stateparticle
BufferDetails: 20mM Tris, 50mM NaCl, 2 mM CaCl2
pH: 7.4
Vitrification
Methodblot for 3 secs
Cryogen NameETHANE
DetailsVitrification instrument: home made plunger
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI TECNAI F30
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeOTHER
Lens
MagnificationNominal: 59000
Imaging ModeOTHER
Defocus900 nm - 3000 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerZEISS SCAI
Number of Digital Images138
Sampling Size7
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmPFT
SoftwarePFT2, EM3DR2
CTF Correctioneach micrograph
Resolution By Author10 A
Resolution MethodFSC 0.5
Single Particle
Details10,000 particle were partitioned into two distinct classes
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body
SoftwareINSOUT
Refinement Protocolrigid body
Refinement SpaceRECIPROCAL
PDB Entry ID1pov
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5122.xml (7.8 KB)
Map dataemd_5122.map.gz (4.3 MB)
Imagesemd_5122_1.tif (1.3 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5122
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, 26.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.2 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 243 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB