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- EMDB-5293: Poliovirus 80S particle and C3 Fab complex at 22 Angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-5293
TitlePoliovirus 80S particle and C3 Fab complex at 22 Angstrom resolution
Map dataThis is a map of poliovirus 80S particle and C3 Fab complex.
Sample
  • Sample: Poliovirus 80S particle and C3 Fab complex
  • Virus: Human poliovirus 1 Mahoney
Keywords80S poliovirus particle / antibody-antigen interactions / antibody-protein interactions / C3 antibody / fragment antibody-binding (Fab) / picornavirus / virus-antibody interactions
Biological speciesHuman poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsLin J / Cheng N / Hogle JM / Steven AC / Belnap DM
CitationJournal: J Immunol / Year: 2013
Title: Conformational shift of a major poliovirus antigen confirmed by immuno-cryogenic electron microscopy.
Authors: Jun Lin / Naiqian Cheng / James M Hogle / Alasdair C Steven / David M Belnap /
Abstract: Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus ...Small, interfacial conformational changes occur in some Ag-Ab interactions. Using cryogenic electron microscopy (cryo-EM), we have demonstrated such changes in a major antigenic site of a poliovirus capsid protein. During cell entry, native human poliovirus (160S particle) converts to a cell entry intermediate (135S particle) and later to an RNA-released (80S) particle. By mixing particles with Fabs of the neutralizing C3 mAb, we labeled the external loop connecting the B and C β-strands (BC loop) of the capsid protein VP1 (residues 95-105) in the 160S and 135S states. We then determined three-dimensional structures by cryo-EM and enhanced their interpretability by fitting high-resolution coordinates of C3 Fab and the capsid proteins into the density maps. Binding of C3 to either 160S or 135S particles caused residues of the BC loop, located on the tip of a prominent peak known as the "mesa," to move by an estimated 5 Å. C3 Abs are neutralizing and can bind bivalently. The orientation of the bound Fabs in our reconstructions suggests that C3 neutralizes poliovirus by binding two adjacent BC loops on the same mesa and inhibiting conformational changes in the viral capsid.
History
DepositionMay 19, 2011-
Header (metadata) releaseOct 26, 2011-
Map releaseMay 31, 2012-
UpdateAug 14, 2013-
Current statusAug 14, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 29.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 29.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5293_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5293.map.gz / Format: CCP4 / Size: 70.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of poliovirus 80S particle and C3 Fab complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.84 Å/pix.
x 267 pix.
= 491.28 Å		1.84 Å/pix.
x 267 pix.
= 491.28 Å		1.84 Å/pix.
x 267 pix.
= 491.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 29.5 / Movie #1: 29.5
Minimum - Maximum-287.460571290000019 - 295.969696039999974
Average (Standard dev.)4.22853899 (±50.462871550000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-133-133-133
Dimensions267267267
Spacing267267267
CellA=B=C: 491.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.841.841.84
M x/y/z267267267
origin x/y/z0.0000.0000.000
length x/y/z491.280491.280491.280
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-287.461295.9704.229

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Supplemental data

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Sample components

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Entire : Poliovirus 80S particle and C3 Fab complex

EntireName: Poliovirus 80S particle and C3 Fab complex
Components
  • Sample: Poliovirus 80S particle and C3 Fab complex
  • Virus: Human poliovirus 1 Mahoney

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Supramolecule #1000: Poliovirus 80S particle and C3 Fab complex

SupramoleculeName: Poliovirus 80S particle and C3 Fab complex / type: sample / ID: 1000 / Oligomeric state: 80S particle icosahedral with Fab / Number unique components: 2

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1
Details: native virus 160S is converted by heat-treatment to 80S
NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 340 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 20 mM Tris, 2 mM CaCl2
VitrificationCryogen name: ETHANE / Instrument: OTHER
Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.
Method: Blotted manually before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Alignment procedureLegacy - Astigmatism: Bsoft
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 14 / Average electron dose: 10 e/Å2 / Details: Defocal pairs were used. / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.77 µm / Nominal defocus min: 1.02 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: phase-flipping CTF correction of each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2
Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
Number images used: 238

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