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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 data
SamplePoliovirus 135S particle:
virus
Function / homology
Function and homology information


suppression by virus of host translation initiation factor activity / suppression by virus of host MDA-5 activity / suppression by virus of host RIG-I activity / 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 MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...suppression by virus of host translation initiation factor activity / suppression by virus of host MDA-5 activity / suppression by virus of host RIG-I activity / 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 MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / positive stranded viral RNA replication / integral to membrane of host cell / pore formation by virus in membrane of host cell / virion assembly / viral capsid / protein complex oligomerization / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / ion channel activity / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / host cell nucleus / structural molecule activity / RNA binding / membrane / ATP binding / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Poliovirus core protein 3a, soluble domain / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Poliovirus core protein 3a, soluble domain / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHuman poliovirus 1 Mahoney (poliovirus)
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

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)
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
Contour LevelPrimary: 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
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, 0.07 M NaCl / pH: 7.5
VitrificationCryogen name: ETHANE / Method: Blotted manually before plunging
Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal), 38500 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Side entry, liquid nitrogen-cooled, cryo specimen holder
Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 12 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8 / Details: Six defocal pairs were scanned.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6850
Details: Defocal pairs were used. Here, corresponding particle images from each micrograph are counted as one.
Applied symmetry: I (正20面体型対称)
3D reconstructionAlgorithm: Fourier Bessel / Software: EM3DR2
CTF correction: CTF and decay correction of each particle image
Resolution: 8.7 Å / Resolution method: FSC 0.333
Euler angles: Determined via PFT2 (used both amplitude and phase information to determine "best" view), focal pairs summed for orientation determination only.
Details: Reconstructed computed from focal pairs. Pairs not summed for reconstruction calculaton.

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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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