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- EMDB-5122: RNA-releasing poliovirus intermediates -

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Basic information

Entry
Database: EMDB / ID: 5122
TitleRNA-releasing poliovirus intermediates
KeywordsPicornavirus / poliovirus / intermediate / RNA-release / 80S
Sample80S poliovirus
Sourcepoliovirus 1 mahoney / virus
Map dataLATE early RNA-releasing 80S poliovirus
Methodsingle particle (icosahedral) reconstruction, at 10 Å resolution
AuthorsLevy HC / Bostina M / Filman DJ / Hogle JM
CitationJ. Virol., 2010, 84, 4426-4441

J. Virol., 2010, 84, 4426-4441 Yorodumi Papers
Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.
Hazel C Levy / Mihnea Bostina / David J Filman / James M Hogle

Validation ReportPDB-ID: 3iyc

SummaryFull reportAbout validation report
DateDeposition: Jun 15, 2009 / Header (metadata) release: Jul 31, 2009 / Map release: Mar 10, 2010 / Last update: Sep 27, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 20.501312207
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 20.501312207
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3iyc
  • Surface level: 20.501312207
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3iyc
  • Imaged by Jmol
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Map

Fileemd_5122.map.gz (map file in CCP4 format, 31723 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
201 pix
2.32 Å/pix.
= 466.782 Å
201 pix
2.32 Å/pix.
= 466.782 Å
201 pix
2.32 Å/pix.
= 466.782 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.3223 Å
Density
Contour Level:2 (by author), 20.5013122 (movie #1):
Minimum - Maximum-29.2078 - 68.0468
Average (Standard dev.)1.89523 (8.2149)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions201201201
Origin-100-100-100
Limit100100100
Spacing201201201
CellA=B=C: 466.782 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS201201201
D min/max/mean-29.20868.0471.895

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Supplemental data

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Sample components

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Entire 80S poliovirus

EntireName: 80S poliovirus / Details: native virus heat-treated at 56 degrees C / Number of components: 1 / Oligomeric State: 60 promoters arranged as a icosahedron
MassTheoretical: 8.3 MDa / Experimental: 8.3 MDa / Measured by: Sedimentation

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Component #1: virus, poliovirus 1 mahoney

VirusName: poliovirus 1 mahoney / a.k.a: poliovirus 1 mahoney / Class: VIRION / Details: native virus is converted by heat-treatment to 80S / Empty: Yes / Enveloped: No / Isolate: SEROTYPE
MassTheoretical: 8.3 MDa / Experimental: 8.3 MDa
SpeciesSpecies: poliovirus 1 mahoney / virus
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES
Shell #1Name of element: capsid / Diameter: 290 Å / T number(triangulation number): 1

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.2 mg/ml / Buffer solution: 20mM Tris, 50mM NaCl, 2 mM CaCl2 / pH: 7.4
Support film200 mesh copper grids
Stainingnot stained
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: blot for 3 secs / Details: Vitrification instrument: home made plunger

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: OTHER
LensMagnification: 59000 X (nominal) / Imaging mode: OTHER / Defocus: 900 - 3000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 138 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction
Details: 10,000 particle were partitioned into two distinct classes
Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: PFT / Software: PFT2, EM3DR2 / CTF correction: each micrograph / Resolution: 10 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: INSOUT / Refinement protocol: rigid body / Refinement space: RECIPROCAL / Details: Protocol: Rigid Body
Input PDB model: 1pov
Output model

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