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Yorodumi- EMDB-1288: Asymmetric binding of transferrin receptor to parvovirus capsids. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1288 | |||||||||
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Title | Asymmetric binding of transferrin receptor to parvovirus capsids. | |||||||||
Map data | Three-dimensional reconstruction of canine parvovirus with bound feline transferrin receptor. | |||||||||
Sample |
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Function / homology | Function and homology information transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / transport across blood-brain barrier / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / RAC3 GTPase cycle / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / osteoclast differentiation / response to nutrient / acute-phase response / cellular response to leukemia inhibitory factor / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / double-stranded RNA binding / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / Clathrin-mediated endocytosis / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / blood microparticle / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Felis silvestris (wild cat) / Canine parvovirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 27.0 Å | |||||||||
Authors | Hafenstein S / Palermo LM / Xiao C / Kostyuchenko VA / Morais M / Nelson CDS / Chipman PR / Bowman VD / Battisti AJ / Parrish CR / Rossmann MG | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1288.map.gz | 48 MB | EMDB map data format | |
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Header (meta data) | emd-1288-v30.xml emd-1288.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | 1288.gif | 15.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1288 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1288 | HTTPS FTP |
-Validation report
Summary document | emd_1288_validation.pdf.gz | 297.8 KB | Display | EMDB validaton report |
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Full document | emd_1288_full_validation.pdf.gz | 297.4 KB | Display | |
Data in XML | emd_1288_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1288 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1288 | HTTPS FTP |
-Related structure data
Related structure data | 2nsuMC 1287C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1288.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Three-dimensional reconstruction of canine parvovirus with bound feline transferrin receptor. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Canine parvovirus complexed with feline transferrin receptor
Entire | Name: Canine parvovirus complexed with feline transferrin receptor |
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Components |
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-Supramolecule #1000: Canine parvovirus complexed with feline transferrin receptor
Supramolecule | Name: 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
Supramolecule | Name: 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 |
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Host (natural) | Organism: Canis lupus (gray wolf) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 280 Å / T number (triangulation number): 1 |
-Macromolecule #1: feline transferrin receptor
Macromolecule | Name: 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 |
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Source (natural) | Organism: Felis silvestris (wild cat) / synonym: Feline |
Recombinant expression | Organism: unidentified baculovirus / Recombinant plasmid: pcDNA 3.1 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 20 mM Tris-HCl |
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Staining | Type: NEGATIVE / Details: no staining |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Temperature | Average: 100 K |
Date | Jan 22, 2003 |
Image recording | Category: 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 min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder: 626 Single Tilt Cryotransfer System / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: CTF correction of each particle |
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Final reconstruction | Applied 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 assignment | 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 ...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 classification | Number classes: 226 |