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- EMDB-1287: Asymmetric binding of transferrin receptor to parvovirus capsids. -

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Basic information

Entry
Database: EMDB / ID: EMD-1287
TitleAsymmetric binding of transferrin receptor to parvovirus capsids.
Map datathe map is multiplied by 1.6 to bring it to the scale of the complexed virus map (EMD-1288)
Sample
  • Sample: empty canine parvovirus particles
  • Virus: Canine parvovirus
Biological speciesCanine parvovirus
Methodsingle particle reconstruction / cryo EM
AuthorsHafenstein S / Palermo LM / Xiao C / Kostyuchenko VA / Morais M / Nelson CDS / Chipman PR / Bowman VD / Battisti AJ / Parrish CR / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2007
Title: Asymmetric binding of transferrin receptor to parvovirus capsids.
Authors: Susan Hafenstein / Laura M Palermo / Victor A Kostyuchenko / Chuan Xiao / Marc C Morais / Christian D S Nelson / Valorie D Bowman / Anthony J Battisti / Paul R Chipman / Colin R Parrish / Michael G Rossmann /
Abstract: Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry ...Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry and conformation of the original infecting virion in preparation for membrane penetration and release of the viral genome. Cryoelectron microscopy and biochemical analyses show that transferrin receptor, the cellular receptor for canine parvovirus, can bind to only one or a few of the 60 icosahedrally equivalent sites on the virion, indicating that either canine parvovirus has inherent asymmetry or binding of receptor induces asymmetry. The asymmetry of receptor binding to canine parvovirus is reminiscent of the special portal in tailed bacteriophages and some large, icosahedral viruses. Asymmetric interactions of icosahedral viruses with their hosts might be a more common phenomenon than previously thought and may have been obscured by averaging in previous crystallographic and electron microscopic structure determinations.
History
DepositionNov 6, 2006-
Header (metadata) releaseNov 6, 2006-
Map releaseMar 21, 2007-
UpdateDec 25, 2013-
Current statusDec 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.609335416
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.609335416
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1287.map.gz / Format: CCP4 / Size: 13.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe map is multiplied by 1.6 to bring it to the scale of the complexed virus map (EMD-1288)
Voxel sizeX=Y=Z: 3.42 Å
Density
Contour LevelBy AUTHOR: 3.48 / Movie #1: 1.6093354
Minimum - Maximum-5.62692785 - 9.40763855
Average (Standard dev.)0.03245007 (±1.5324012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-76-76-76
Dimensions152152152
Spacing152152152
CellA=B=C: 519.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z152152152
origin x/y/z0.0000.0000.000
length x/y/z519.840519.840519.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-76-76-76
NC/NR/NS152152152
D min/max/mean-5.6279.4080.032

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Supplemental data

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Sample components

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Entire : empty canine parvovirus particles

EntireName: empty canine parvovirus particles
Components
  • Sample: empty canine parvovirus particles
  • Virus: Canine parvovirus

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Supramolecule #1000: empty canine parvovirus particles

SupramoleculeName: empty canine parvovirus particles / type: sample / ID: 1000 / Oligomeric state: icosahedral virus particles / Number unique components: 1

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Supramolecule #1: Canine parvovirus

SupramoleculeName: Canine parvovirus / type: virus / ID: 1 / Name.synonym: CPV / Details: empty virus capsids / NCBI-ID: 10788 / Sci species name: Canine parvovirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: CPV
Host (natural)synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: capsid / Diameter: 280 Å / T number (triangulation number): 3

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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: 20mM Tris-HCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder: 626 Single Tilt Cryotransfer System / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
DateMay 6, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 3 / Average electron dose: 18 e/Å2
Details: images were scanned at 7 micron sampling step size followed by 2x2 averaging to produce 14 micron step size
Bits/pixel: 8

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Image processing

CTF correctionDetails: CTF correction of each particle
Final two d classificationNumber classes: 226
Final angle assignmentDetails: initial angles were selected using SPIDER VO EA procedure with limits for theta of 0-40, phi of 0-72 to cover an asymmetric unit of an icosahedron; During orientation search the angles were ...Details: initial angles were selected using SPIDER VO EA procedure with limits for theta of 0-40, phi of 0-72 to cover an asymmetric unit of an icosahedron; During orientation search the angles were changed to be one of the 60 icosahedral symmetry equivalent triplet.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Software - Name: XMIPP with modifications
Details: Intermediate reconstructions were made from images with virus density subtracted, final reconstruction was calculated from complete images.
Number images used: 2027

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