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- EMDB-5286: Poliovirus 80S particle and P1 Fab complex with Fab bound at prop... -

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Basic information

Entry
Database: EMDB / ID: EMD-5286
TitlePoliovirus 80S particle and P1 Fab complex with Fab bound at propeller tip
Map data
SamplePoliovirus 80S particle and P1(monospecific antibody) Fab complex:
virus
Keywordspicornavirus / viral cell entry / viral uncoating / virus-antibody complex / virus-Fab complex / virus disassembly / virus uncoating / virus conformational transitions / monospecific antibody
Biological speciesHuman poliovirus 1 Mahoney (poliovirus 80S)
Methodsingle particle reconstruction / cryo EM / Resolution: 18 Å
AuthorsLin J / Cheng N / Chow M / Filman DJ / Steven AC / Hogle JM / Belnap DM
CitationJournal: J. Virol. / Year: 2011
Title: An externalized polypeptide partitions between two distinct sites on genome-released poliovirus particles.
Authors: Jun Lin / Naiqian Cheng / Marie Chow / David J Filman / Alasdair C Steven / James M Hogle / David M Belnap /
Abstract: During cell entry, native poliovirus (160S) converts to a cell-entry intermediate (135S) particle, resulting in the externalization of capsid proteins VP4 and the amino terminus of VP1 (residues 1 to ...During cell entry, native poliovirus (160S) converts to a cell-entry intermediate (135S) particle, resulting in the externalization of capsid proteins VP4 and the amino terminus of VP1 (residues 1 to 53). Externalization of these entities is followed by release of the RNA genome (uncoating), leaving an empty (80S) particle. The antigen-binding fragment (Fab) of a monospecific peptide 1 (P1) antibody, which was raised against a peptide corresponding to amino-terminal residues 24 to 40 of VP1, was utilized to track the location of the amino terminus of VP1 in the 135S and 80S states of poliovirus particles via cryogenic electron microscopy (cryo-EM) and three-dimensional image reconstruction. On 135S, P1 Fabs bind to a prominent feature on the external surface known as the "propeller tip." In contrast, our initial 80S-P1 reconstruction showed P1 Fabs also binding to a second site, at least 50 Å distant, at the icosahedral 2-fold axes. Further analysis showed that the overall population of 80S-P1 particles consisted of three kinds of capsids: those with P1 Fabs bound only at the propeller tips, P1 Fabs bound only at the 2-fold axes, or P1 Fabs simultaneously bound at both positions. Our results indicate that, in 80S particles, a significant fraction of VP1 can deviate from icosahedral symmetry. Hence, this portion of VP1 does not change conformation synchronously when switching from the 135S state. These conclusions are compatible with previous observations of multiple conformations of the 80S state and suggest that movement of the amino terminus of VP1 has a role in uncoating. Similar deviations from icosahedral symmetry may be biologically significant during other viral transitions.
History
DepositionMay 2, 2011-
Header (metadata) releaseMay 5, 2011-
Map releaseMar 8, 2012-
UpdateOct 3, 2012-
Current statusOct 3, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 11.32
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5286.map.gz / Format: CCP4 / Size: 70.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.83 Å/pix.
x 267 pix.
= 488.61 Å
1.83 Å/pix.
x 267 pix.
= 488.61 Å
1.83 Å/pix.
x 267 pix.
= 488.61 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.83 Å
Density
Contour LevelBy AUTHOR: 11.32 / Movie #1: 11.32
Minimum - Maximum-32.757297520000002 - 90.331504820000006
Average (Standard dev.)3.17764044 (±16.409234999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-133-133-133
Dimensions267267267
Spacing267267267
CellA=B=C: 488.61002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.831.831.83
M x/y/z267267267
origin x/y/z0.0000.0000.000
length x/y/z488.610488.610488.610
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-133-133-133
NC/NR/NS267267267
D min/max/mean-32.75790.3323.178

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Supplemental data

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Sample components

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Entire Poliovirus 80S particle and P1(monospecific antibody) Fab complex

EntireName: Poliovirus 80S particle and P1(monospecific antibody) Fab complex
Number of components: 2 / Oligomeric State: 80S particle icosahedral with Fab

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Component #1: virus, Human poliovirus 1 Mahoney

VirusName: Human poliovirus 1 Mahoney / a.k.a: poliovirus 80S / Class: VIRION
Details: native virus 160S is converted by heat-treatment to 80S
Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Human poliovirus 1 Mahoney (poliovirus 80S)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Tris, 2 mM CaCl2 / 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 / Date: Jul 15, 1999
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal), 37752 X (calibrated) / Astigmatism: Bsoft / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 810 - 2240 nm
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: 14 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8 / Details: Defocal pairs were used.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1132 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Fourier Bessel / Software: EM3DR2 / CTF correction: CTF and decay correction of each particle
Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Resolution: 18 Å / Resolution method: FSC 0.5

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