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- EMDB-1136: The structure of the poliovirus 135S cell entry intermediate at 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-1136
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 particle produced by heating 160S particles at 50 deg. C for 3 minutes. 135S particles treated with Staphylococcus areus V8 protease. Buffer: 10 mM HEPES, 2 mM CaCl2, 0.07M NaCl, pH 7.5. Images corrected for contrast transfer function and decay before reconstruction.
Sample
  • Sample: Poliovirus 135S particle
  • Virus: Human poliovirus 1 Mahoney
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHuman poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 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.
History
DepositionNov 8, 2004-
Header (metadata) releaseJul 15, 2005-
Map releaseJul 21, 2005-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 150
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 150
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1xyr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1136.gif

Downloads & links

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Map

FileDownload / File: emd_1136.map.gz / Format: CCP4 / Size: 28.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPoliovirus 135S particle produced by heating 160S particles at 50 deg. C for 3 minutes. 135S particles treated with Staphylococcus areus V8 protease. Buffer: 10 mM HEPES, 2 mM CaCl2, 0.07M NaCl, pH 7.5. Images corrected for contrast transfer function and decay before reconstruction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.82 Å/pix.
x 197 pix.
= 356.72 Å		1.82 Å/pix.
x 197 pix.
= 356.72 Å		1.82 Å/pix.
x 197 pix.
= 356.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.82 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 194.0 / Movie #1: 150
Minimum - Maximum-121.641000000000005 - 312.184000000000026
Average (Standard dev.)34.7164 (±74.369799999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-98-98-98
Dimensions197197197
Spacing197197197
CellA=B=C: 356.72 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.821.821.82
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z356.720356.720356.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-98-98-98
NC/NR/NS197197197
D min/max/mean-121.641312.18434.716

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Supplemental data

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Sample components

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Entire : Poliovirus 135S particle

EntireName: Poliovirus 135S particle
Components
  • Sample: Poliovirus 135S particle
  • Virus: Human poliovirus 1 Mahoney

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Supramolecule #1000: Poliovirus 135S particle

SupramoleculeName: Poliovirus 135S particle / type: sample / ID: 1000
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 unique components: 1

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1 / Name.synonym: poliovirus / Details: 135S particle / NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: poliovirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: capsid / Diameter: 339 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 20 mM HEPES, 2 mM CaCl2, 0.07 M NaCl
VitrificationCryogen name: ETHANE
Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.
Method: Blotted manually before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 12 / Average electron dose: 10 e/Å2 / Details: Six defocal pairs were scanned. / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry, liquid nitrogen-cooled, cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsDefocal pairs were used. Here, corresponding particle images from each micrograph are counted as one.
CTF correctionDetails: CTF and decay correction of each particle image
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: EM3DR2
Details: Reconstructed computed from focal pairs. Pairs not summed for reconstruction calculaton.
Number images used: 6850
Final angle assignmentDetails: Determined via PFT2 (used both amplitude and phase information to determine "best" view), focal pairs summed for orientation determination only.

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Atomic model buiding 1

DetailsProtocol: rigid body. see paper for details of the model fitting
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-1xyr:
Poliovirus 135S cell entry intermediate

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