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- EMDB-1144: The structure of the poliovirus 135S cell entry intermediate at 1... -

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Entry
Database: EMDB / ID: 1144
TitleThe structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes.
Map dataPoliovirus 135S cell-entry intermediate produced by heating native virus for 3min. 50 degrees in 20mM HEPES pH 7.4, 2mM CaCl2
SamplePoliovirus 135S particle:
virus
Function / homologyPoliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein ...Poliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein / Picornavirus 2B protein / 3C cysteine protease (picornain 3C) / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / RNA dependent RNA polymerase / RNA helicase / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3, picornavirus core protein 2A / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / T=pseudo3 icosahedral viral capsid / 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 / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
SourceHuman poliovirus 1 Mahoney (poliovirus)
Methodsingle particle reconstruction / cryo EM / 11 Å resolution
AuthorsBubeck D / Filman DJ / Cheng N / Steven AC / Hogle JM / Belnap DM
CitationJournal: J. Virol. / Year: 2005
Title: The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes.
Authors: Doryen Bubeck / David J Filman / Naiqian Cheng / Alasdair C Steven / James M Hogle / David M Belnap
Validation ReportPDB-ID: 1xyr

SummaryFull reportAbout validation report
DateDeposition: Nov 6, 2004 / Header (metadata) release: Aug 4, 2005 / Map release: Sep 2, 2005 / Last update: Oct 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 90
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 90
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-1xyr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1144.map.gz (map file in CCP4 format, 10114 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
173 pix
2.69 Å/pix.
= 465.37 Å
173 pix
2.69 Å/pix.
= 465.37 Å
173 pix
2.69 Å/pix.
= 465.37 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.69 Å
Density
Contour Level:92.9, 90 (movie #1):
Minimum - Maximum-324 - 425
Average (Standard dev.)6.30321 (48.9107)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions173173173
Origin-86-86-86
Limit868686
Spacing173173173
CellA=B=C: 465.37 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.692.692.69
M x/y/z173173173
origin x/y/z0.0000.0000.000
length x/y/z465.370465.370465.370
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-86-86-86
NC/NR/NS173173173
D min/max/mean-324.000425.0006.303

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Supplemental data

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Sample components

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Entire Poliovirus 135S particle

EntireName: Poliovirus 135S particle
Details: Sedimentation coefficient = 135S. Poliovirus 135S particle produced by heating 160S particles at 50 deg. C for 3 minutes.
Oligomeric State: icosahedrally ordered capsid, 60 copies of VP1, VP2, VP3
Number of components: 1

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Component #1: virus, Human poliovirus 1 Mahoney

VirusName: Human poliovirus 1 Mahoney / a.k.a: poliovirus / Class: VIRION / Details: 135S particle / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Human poliovirus 1 Mahoney (poliovirus)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: capsid / Diameter: 339 Å / T number(triangulation number): 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM HEPES, 2 mM CaCl2 / pH: 7.4
VitrificationCryogen name: ETHANE / Method: Plunge frozen in liquid ethane. / Details: Vitrification occurred in ambient atmosphere.

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Side entry, liquid nitrogen-cooled, cryo specimen holder
Model: GATAN LIQUID NITROGEN

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Image acquisition

Image acquisitionNumber of digital images: 44 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / Details: 22 defocal pairs were scanned.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3641
Details: Defocal pairs were used. Here, corresponding particle images from each micrograph are counted as one.
Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Fourier Bessel / Software: EM3DR2
CTF correction: CTF and decay correction of each particle image
Resolution: 11 Å / Resolution method: FSC 0.333
Euler angles: Determined via PFT2 (used both amplitude and phase information to determine "best" view).

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: RECIPROCAL
Details: Protocol: rigid body. see paper for details of the model fitting
Output model

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