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- EMDB-5387: Structure of the Fab-Labeled 'Breathing' State of Native Poliovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-5387
TitleStructure of the Fab-Labeled 'Breathing' State of Native Poliovirus
Map dataStructure of the Fab-Labeled 'Breathing' State of Native Poliovirus
Sample
  • Sample: Poliovirus 160S particle at 37 degrees C, Fab complex
  • Virus: Human poliovirus 1 Mahoney
Keywordsreversible conformational change / picornavirus / viral cell entry / virus-Fab complex / virus-antibody complex
Biological speciesHuman poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsLin J / Lee L / Roivainen M / Filman DJ / Hogle JM / Belnap DM
CitationJournal: J Virol / Year: 2012
Title: Structure of the Fab-labeled "breathing" state of native poliovirus.
Authors: Jun Lin / Lily Y Lee / Merja Roivainen / David J Filman / James M Hogle / David M Belnap /
Abstract: At 37°C, the structure of poliovirus is dynamic, and internal polypeptides VP4 and N terminus of VP1 (residues 1 to 53) externalize reversibly. An Fab fragment of a monospecific antibody, which ...At 37°C, the structure of poliovirus is dynamic, and internal polypeptides VP4 and N terminus of VP1 (residues 1 to 53) externalize reversibly. An Fab fragment of a monospecific antibody, which binds to residues 39 to 55 of VP1, was utilized to locate the N termini of VP1 in native (160S) particles in this "breathing" state. Fab and virus were mixed and imaged via cryogenic electron microscopy. The resulting reconstruction showed the capsid expands similarly to the irreversibly altered cell entry intermediate (135S) particle, but the N terminus of VP1 is located near the 2-fold axes, instead of the "propeller tip" as in 135S particles.
History
DepositionJan 30, 2012-
Header (metadata) releaseFeb 13, 2013-
Map releaseFeb 13, 2013-
UpdateFeb 13, 2013-
Current statusFeb 13, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5387_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5387.map.gz / Format: CCP4 / Size: 70.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the Fab-Labeled 'Breathing' State of Native Poliovirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 267 pix.
= 435.21 Å		1.63 Å/pix.
x 267 pix.
= 435.21 Å		1.63 Å/pix.
x 267 pix.
= 435.21 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.3 / Movie #1: 5.3
Minimum - Maximum-16.280876159999998 - 48.292263030000001
Average (Standard dev.)5.32685471 (±12.5979147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-133-133-133
Dimensions267267267
Spacing267267267
CellA=B=C: 435.21 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z267267267
origin x/y/z0.0000.0000.000
length x/y/z435.210435.210435.210
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-16.28148.2925.327

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Supplemental data

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Sample components

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Entire : Poliovirus 160S particle at 37 degrees C, Fab complex

EntireName: Poliovirus 160S particle at 37 degrees C, Fab complex
Components
  • Sample: Poliovirus 160S particle at 37 degrees C, Fab complex
  • Virus: Human poliovirus 1 Mahoney

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Supramolecule #1000: Poliovirus 160S particle at 37 degrees C, Fab complex

SupramoleculeName: Poliovirus 160S particle at 37 degrees C, Fab complex / type: sample / ID: 1000 / Oligomeric state: 160S 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
Name.synonym: Poliovirus type 1 (strain Mahoney), human poliovirus 1 strain Mahoney
NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Syn species name: Poliovirus type 1 (strain Mahoney), human poliovirus 1 strain Mahoney
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / 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: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F30
Alignment procedureLegacy - Astigmatism: Bsoft
DateOct 1, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 7 µm / Number real images: 7 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.037 µm / Nominal defocus min: 2.395 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF and decay correct
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2 / Number images used: 137

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