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- EMDB-5280: Poliovirus 135S particle and P1 Fab complex at 12-angs. resolution -

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Database: EMDB / ID: EMD-5280
TitlePoliovirus 135S particle and P1 Fab complex at 12-angs. resolution
Map data
SamplePoliovirus 135S particle and P1(monospecific antibody) Fab complex:
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 135S)
Methodsingle particle reconstruction / cryo EM / Resolution: 12 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.
DepositionMay 2, 2011-
Header (metadata) releaseMay 5, 2011-
Map releaseMar 8, 2012-
UpdateOct 3, 2012-
Current statusOct 3, 2012Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 8.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 8.6
  • Imaged by UCSF Chimera
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Structure viewerEM map:
Supplemental images

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FileDownload / File: emd_5280.map.gz / Format: CCP4 / Size: 70.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.83 Å
Contour LevelBy AUTHOR: 8.6 / Movie #1: 8.6
Minimum - Maximum-31.677835460000001 - 96.891075130000004
Average (Standard dev.)5.0518713 (±17.715793609999999)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
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
start NX/NY/NZ-62-62-62
MAP C/R/S123
start NC/NR/NS-133-133-133
D min/max/mean-31.67896.8915.052

Supplemental data

Sample components

Entire Poliovirus 135S particle and P1(monospecific antibody) Fab complex

EntireName: Poliovirus 135S particle and P1(monospecific antibody) Fab complex
Number of components: 2 / Oligomeric State: 135S particle icosahedral with Fab

Component #1: virus, Human poliovirus 1 Mahoney

VirusName: Human poliovirus 1 Mahoney / a.k.a: poliovirus 135S / Class: VIRION
Details: native virus 160S is converted by heat-treatment to 135S
Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Human poliovirus 1 Mahoney (poliovirus 135S)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

Experimental details

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.

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
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 14 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8 / Details: Defocal pairs were used.

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 10160 / 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
Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Resolution: 12 Å / Resolution method: FSC 0.5

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