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- EMDB-1288: Asymmetric binding of transferrin receptor to parvovirus capsids. -

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Basic information

Entry
Database: EMDB / ID: EMD-1288
TitleAsymmetric binding of transferrin receptor to parvovirus capsids.
Map dataThree-dimensional reconstruction of canine parvovirus with bound feline transferrin receptor.
Sample
  • Sample: Canine parvovirus complexed with feline transferrin receptor
  • Virus: Canine parvovirus 2
  • Protein or peptide: feline transferrin receptor
Function / homology
Function and homology information


transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / response to manganese ion ...transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of bone resorption / regulation of postsynaptic membrane neurotransmitter receptor levels / transport across blood-brain barrier / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / response to nutrient / Hsp70 protein binding / osteoclast differentiation / cellular response to leukemia inhibitory factor / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / recycling endosome / receptor internalization / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / extracellular vesicle / double-stranded RNA binding / Clathrin-mediated endocytosis / iron ion transport / virus receptor activity / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / intracellular iron ion homeostasis / positive regulation of canonical NF-kappaB signal transduction / early endosome / response to hypoxia / endosome / endosome membrane / intracellular signal transduction / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Transferrin receptor protein 1
Similarity search - Component
Biological speciesFelis silvestris (wild cat) / Canine parvovirus 2
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 27.0 Å
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 1, 2006-
Header (metadata) releaseNov 6, 2006-
Map releaseMar 21, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.98545839
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.98545839
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2nsu
  • Surface level: 1.98545839
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2nsu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1288.gif

Downloads & links

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Map

FileDownload / File: emd_1288.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree-dimensional reconstruction of canine parvovirus with bound feline transferrin receptor.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 256 pix.
= 665.6 Å		2.6 Å/pix.
x 256 pix.
= 665.6 Å		2.6 Å/pix.
x 256 pix.
= 665.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.5 / Movie #1: 1.9854584
Minimum - Maximum-3.0484 - 9.01338
Average (Standard dev.)0.000000000238234 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 665.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z665.600665.600665.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-3.0489.0130.000

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Supplemental data

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Sample components

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Entire : Canine parvovirus complexed with feline transferrin receptor

EntireName: Canine parvovirus complexed with feline transferrin receptor
Components
  • Sample: Canine parvovirus complexed with feline transferrin receptor
  • Virus: Canine parvovirus 2
  • Protein or peptide: feline transferrin receptor

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Supramolecule #1000: Canine parvovirus complexed with feline transferrin receptor

SupramoleculeName: Canine parvovirus complexed with feline transferrin receptor
type: sample / ID: 1000
Oligomeric state: one homodimer of fTfR binds to one icosahedral CPV particle
Number unique components: 2

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Supramolecule #1: Canine parvovirus 2

SupramoleculeName: Canine parvovirus 2 / type: virus / ID: 1 / Name.synonym: CPV / Details: empty capsids / NCBI-ID: 246878 / Sci species name: Canine parvovirus 2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: CPV
Host (natural)Organism: Canis lupus (gray wolf) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: capsid / Diameter: 280 Å / T number (triangulation number): 1

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Macromolecule #1: feline transferrin receptor

MacromoleculeName: feline transferrin receptor / type: protein_or_peptide / ID: 1 / Name.synonym: feTfR / Details: ectodomain only / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Felis silvestris (wild cat) / synonym: Feline
Recombinant expressionOrganism: unidentified baculovirus / Recombinant plasmid: pcDNA 3.1

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 20 mM Tris-HCl
StainingType: NEGATIVE / Details: no staining
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 100 K
DateJan 22, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 115 / Average electron dose: 25.96 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 54000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: 626 Single Tilt Cryotransfer System / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: CTF correction of each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / 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: 8566
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 two d classificationNumber classes: 226

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