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- EMDB-5123: RNA-releasing poliovirus intermediates -

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Basic information

Entry
Database: EMDB / ID: 5123
TitleRNA-releasing poliovirus intermediates
Map datathis is poliovirus in the early stage of RNA release
Sample80S poliovirus:
virus
KeywordsPicornavirus / poliovirus / intermediate / RNA release / 80S
Function / homologyViral coat protein subunit / 3C cysteine protease (picornain 3C) / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A ...Viral coat protein subunit / 3C cysteine protease (picornain 3C) / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus 3A protein-like / Peptidase S1, PA clan / RdRp of positive ssRNA viruses catalytic domain profile. / Picornavirus core protein 2A / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / P-loop containing nucleoside triphosphate hydrolase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Picornavirus 2B protein / RNA helicase / RNA dependent RNA polymerase / caveolin-mediated endocytosis of virus by host cell / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / T=pseudo3 icosahedral viral capsid / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / suppression by virus of host gene expression / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / DNA replication / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
Sourcepoliovirus 1 mahoney (poliovirus 1 mahoney)
Methodsingle particle reconstruction / cryo EM / negative staining / 10 Å resolution
AuthorsLevy HC / Bostina M / Filman DJ / Hogle JM
CitationJournal: J. Virol. / Year: 2010
Title: Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.
Authors: Hazel C Levy / Mihnea Bostina / David J Filman / James M Hogle
Validation ReportPDB-ID: 3iyb

SummaryFull reportAbout validation report
DateDeposition: Jul 16, 2009 / Header (metadata) release: Jul 31, 2009 / Map release: Mar 10, 2010 / Last update: Sep 23, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
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  • Surface view with fitted model
  • Atomic models: : PDB-3iyb
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3iyb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5123.map.gz (map file in CCP4 format, 31723 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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.

Voxel sizeX=Y=Z: 2.3223 Å
Density
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-40.0586 - 80.741
Average (Standard dev.)1.8502 (8.19719)
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-40.05980.7411.850

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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 / Empty: Yes / Enveloped: No / Isolate: SEROTYPE
MassTheoretical: 8.3 MDa / Experimental: 8.3 MDa
SpeciesSpecies: poliovirus 1 mahoney (poliovirus 1 mahoney)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: VP1 VP2 and VP3 / Diameter: 290 Å / T number(triangulation number): 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
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 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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