+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5179 | |||||||||
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Title | The Interaction of Decay-accelerating Factor with Echovirus 7 | |||||||||
Map data | CryoEM reconstruction of human echovirus in complex with its cellular receptor DAF. (The map has positive values in regions of protein and nucleic acid density.) | |||||||||
Sample |
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Keywords | VIRUS / RECEPTOR / COMPLEX / ECHOVIRUS / DAF / ICOSAHEDRAL VIRUS | |||||||||
Function / homology | Function and homology information regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / complement activation, classical pathway / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / symbiont-mediated suppression of host gene expression / viral capsid / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / DNA replication / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / membrane raft / induction by virus of host autophagy / Golgi membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / innate immune response / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human echovirus 7 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | PLEVKA P / HAFENSTEIN S / ZHANG Y / HARRIS KG / CIEFUENTE JO / BOWMAN VD / CHIPMAN PR / LIN F / MEDOF DE / BATOR CM / ROSSMANN MG | |||||||||
Citation | Journal: J Virol / Year: 2010 Title: Interaction of decay-accelerating factor with echovirus 7. Authors: Pavel Plevka / Susan Hafenstein / Katherine G Harris / Javier O Cifuente / Ying Zhang / Valorie D Bowman / Paul R Chipman / Carol M Bator / Feng Lin / M Edward Medof / Michael G Rossmann / Abstract: Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral ...Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral uncoating during infection. However, in addition, some of the enteroviruses use an alternative or additional receptor that binds outside the canyon. Decay-accelerating factor (DAF) has been identified as a cellular receptor for EV7. The crystal structure of EV7 has been determined to 3.1-Å resolution and used to interpret the 7.2-Å-resolution cryo-electron microscopy reconstruction of EV7 complexed with DAF. Each DAF binding site on EV7 is near a 2-fold icosahedral symmetry axis, which differs from the binding site of DAF on the surface of coxsackievirus B3, indicating that there are independent evolutionary processes by which DAF was selected as a picornavirus accessory receptor. This suggests that there is an advantage for these viruses to recognize DAF during the initial process of infection. | |||||||||
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_5179.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-5179-v30.xml emd-5179.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_5179_1.jpg | 73.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5179 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5179 | HTTPS FTP |
-Validation report
Summary document | emd_5179_validation.pdf.gz | 313.7 KB | Display | EMDB validaton report |
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Full document | emd_5179_full_validation.pdf.gz | 313.3 KB | Display | |
Data in XML | emd_5179_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5179 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5179 | HTTPS FTP |
-Related structure data
Related structure data | 3iypMC 2x5iC 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_5179.map.gz / Format: CCP4 / Size: 19.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM reconstruction of human echovirus in complex with its cellular receptor DAF. (The map has positive values in regions of protein and nucleic acid density.) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.65 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 : Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)
Entire | Name: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF) |
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Components |
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-Supramolecule #1000: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)
Supramolecule | Name: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF) type: sample / ID: 1000 Oligomeric state: one DAF molecule binds to one asymmetric unit of EV7 Number unique components: 2 |
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Molecular weight | Theoretical: 6.8 MDa |
-Supramolecule #1: Human echovirus 7
Supramolecule | Name: Human echovirus 7 / type: virus / ID: 1 / Name.synonym: human echovirus 7 / NCBI-ID: 46018 / Sci species name: Human echovirus 7 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: human echovirus 7 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 5.2 MDa |
Virus shell | Shell ID: 1 / Diameter: 320 Å / T number (triangulation number): 1 |
-Macromolecule #1: Decay Accelerating Factor
Macromolecule | Name: Decay Accelerating Factor / type: protein_or_peptide / ID: 1 / Name.synonym: DAF / Number of copies: 60 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane |
Molecular weight | Theoretical: 26 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) / Recombinant plasmid: pPICZaA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.2 / Details: 0.1 M NaCl, 20mM Tris |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 113 K / Instrument: OTHER Timed resolved state: Vitrified 1 hour after mixing DAF with EV7 Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Temperature | Average: 100 K |
Details | Micrographs were digitized with a Zeiss PHODIS microdensitometer at 7-micron intervals. |
Date | Jan 1, 2000 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 81 / Average electron dose: 20 e/Å2 / Details: The scans were averaged in boxes of 2x2 pixels. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.67 µm / Nominal defocus min: 1.12 µm |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder. Specimen holder model: OTHER |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem / Number images used: 11430 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | EV7 capsid protein coordinates were positioned into the cryoEM reconstruction by superimposing icosahedral symmetry elements. |
Refinement | Space: REAL |
Output model | PDB-3iyp: |