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

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Basic information

Entry
Database: EMDB / ID: 5280
TitlePoliovirus 135S particle and P1 Fab complex at 12-angs. resolution
Keywordspicornavirus / viral cell entry / viral uncoating / virus-antibody complex / virus-Fab complex / virus disassembly / virus uncoating / virus conformational transitions / monospecific antibody
SamplePoliovirus 135S particle and P1(monospecific antibody) Fab complex
SourceHuman poliovirus 1 Mahoney / virus / poliovirus 135S
Map dataThis is a map of poliovirus 135S and P1 Fab complex at 12-ang resolution
Methodsingle particle (icosahedral) reconstruction, at 12 A resolution
AuthorsLin J / Cheng N / Chow M / Filman DJ / Steven AC / Hogle JM / Belnap DM
CitationJ. Virol., 2011, 85, 9974-9983

J. Virol., 2011, 85, 9974-9983 StrPapers
An externalized polypeptide partitions between two distinct sites on genome-released poliovirus particles.
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: May 2, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 8.6
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5280.map.gz (map file in CCP4 format, 74354 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
267 pix
1.83 A/pix
= 488.61 A
267 pix
1.83 A/pix
= 488.61 A
267 pix
1.83 A/pix
= 488.61 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.83 A
Density
Contour Level:8.6 (by author), 8.6 (movie #1):
Minimum - Maximum-31.67783546 - 96.89107513
Average (Standard dev.)5.0518713 (17.71579361)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions267267267
Origin-133-133-133
Limit133133133
Spacing267267267
CellA=B=C: 488.61002 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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-31.67896.8915.052

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Supplemental data

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Sample components

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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

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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 / virus / poliovirus 135S
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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Experimental details

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Sample preparation

Specimen stateparticle
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.

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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/A2 / 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 microns / Bit depth: 8 / Details: Defocal pairs were used.

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 10160 / 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: 12 A / Resolution method: FSC 0.5

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