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- EMDB-5283: Poliovirus 80S particle and P1 Fab complex at 13-angs. resolution -

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Basic information

Database: EMDB / ID: 5283
TitlePoliovirus 80S particle and P1 Fab complex at 13-angs. resolution
Map dataThis is a map of poliovirus 80S particle and P1 Fab complex at 13-angs resolution
SamplePoliovirus 80S 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
SourceHuman poliovirus 1 Mahoney (poliovirus 80S)
Methodsingle particle reconstruction / cryo EM / 13 Å resolution
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
DateDeposition: May 2, 2011 / Header (metadata) release: May 5, 2011 / Map release: Mar 8, 2012 / Last update: Oct 3, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 11.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 11.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_5283.map.gz (map file in CCP4 format, 74354 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
267 pix
1.83 Å/pix.
= 488.61 Å
267 pix
1.83 Å/pix.
= 488.61 Å
267 pix
1.83 Å/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 Level:11.7 (by author), 11.7 (movie #1):
Minimum - Maximum-31.98928070 - 106.81854248
Average (Standard dev.)3.31379390 (16.79324913)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 488.61002 Å
α=β=γ: 90.0 deg.

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-31.989106.8193.314

Supplemental data

Sample components

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

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

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Tris, 2 mM CaCl2 / pH: 7.5
VitrificationInstrument: NONE / Cryogen 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 microns / Bit depth: 8 / Details: Defocal pairs were used.

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 5256 / 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: 13 Å / Resolution method: FSC 0.5

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