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

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Basic information

Entry
Database: EMDB / ID: EMD-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 data
SamplePoliovirus 135S particle:
virus
Function / homology
Function and homology information


suppression by virus of host MDA-5 activity / 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 / suppression by virus of host RIG-I activity / picornain 3C / suppression by virus of host MAVS activity / T=pseudo3 icosahedral viral capsid ...suppression by virus of host MDA-5 activity / 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 / suppression by virus of host RIG-I activity / picornain 3C / suppression by virus of host MAVS activity / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / protein complex oligomerization / induction by virus of host autophagy / RNA-directed RNA polymerase / ion channel activity / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus 2B protein / Picornavirus capsid / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded DNA/RNA virus / P-loop containing nucleoside triphosphate hydrolase ...Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus 2B protein / Picornavirus capsid / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded DNA/RNA virus / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / RNA-directed RNA polymerase, C-terminal domain / Peptidase C3, picornavirus core protein 2A
Genome polyprotein
Biological speciesHuman poliovirus 1 Mahoney (poliovirus)
Methodsingle particle reconstruction / cryo EM / Resolution: 11 Å
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 /
Abstract: Poliovirus provides a well-characterized system for understanding how nonenveloped viruses enter and infect cells. Upon binding its receptor, poliovirus undergoes an irreversible conformational ...Poliovirus provides a well-characterized system for understanding how nonenveloped viruses enter and infect cells. Upon binding its receptor, poliovirus undergoes an irreversible conformational change to the 135S cell entry intermediate. This transition involves shifts of the capsid protein beta barrels, accompanied by the externalization of VP4 and the N terminus of VP1. Both polypeptides associate with membranes and are postulated to facilitate entry by forming a translocation pore for the viral RNA. We have calculated cryo-electron microscopic reconstructions of 135S particles that permit accurate placement of the beta barrels, loops, and terminal extensions of the capsid proteins. The reconstructions and resulting models indicate that each N terminus of VP1 exits the capsid though an opening in the interface between VP1 and VP3 at the base of the canyon that surrounds the fivefold axis. Comparison with reconstructions of 135S particles in which the first 31 residues of VP1 were proteolytically removed revealed that the externalized N terminus is located near the tips of propeller-like features surrounding the threefold axes rather than at the fivefold axes, as had been proposed in previous models. These observations have forced a reexamination of current models for the role of the 135S particle in transmembrane pore formation and suggest testable alternatives.
Validation ReportPDB-ID: 1xyr

SummaryFull reportAbout validation report
History
Current status-Processing site: PDBe / Status: Released
DepositionNov 6, 2004-
Header (metadata) releaseAug 4, 2005-
Map releaseSep 2, 2005-
UpdateOct 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

FileDownload / File: emd_1144.map.gz / Format: CCP4 / Size: 9.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.69 Å/pix.
x 173 pix.
= 465.37 Å
2.69 Å/pix.
x 173 pix.
= 465.37 Å
2.69 Å/pix.
x 173 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 LevelPrimary: 92.900000000000006 / Movie #1: 90
Minimum - Maximum-324.0 - 425.0
Average (Standard dev.)6.30321 (±48.910699999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-86-86-86
Dimensions173173173
Spacing173173173
CellA=B=C: 465.37 Å
α=β=γ: 90 °

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 µm / 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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