+Open data
-Basic information
Entry | Database: PDB / ID: 3iyp | ||||||
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Title | The Interaction of Decay-accelerating Factor with Echovirus 7 | ||||||
Components |
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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 | Human echovirus 7 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å | ||||||
Authors | Plevka, P. / Hafenstein, S. / Zhang, Y. / Harris, K.G. / Cifuente, J.O. / Bowman, V.D. / Chipman, P.R. / Lin, F. / Medof, D.E. / Bator, C.M. / Rossmann, M.G. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3iyp.cif.gz | 226.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iyp.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 3iyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iyp_validation.pdf.gz | 744.2 KB | Display | wwPDB validaton report |
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Full document | 3iyp_full_validation.pdf.gz | 787.8 KB | Display | |
Data in XML | 3iyp_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 3iyp_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/3iyp ftp://data.pdbj.org/pub/pdb/validation_reports/iy/3iyp | HTTPS FTP |
-Related structure data
Related structure data | 5179MC 2x5iC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Protein , 5 types, 5 molecules ABCDF
#1: Protein | Mass: 33313.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q9QP24 |
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#2: Protein | Mass: 26226.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q6W9E5 |
#3: Protein | Mass: 29072.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q6W9E5 |
#4: Protein | Mass: 7599.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q91QV1 |
#5: Protein | Mass: 41511.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08174 |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-DAO / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 6.8 MDa / Experimental value: NO | |||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION | |||||||||||||||
Natural host | Organism: Homo sapiens | |||||||||||||||
Buffer solution | Name: 0.1 M NaCl, 20mM Tris / pH: 7.2 / Details: 0.1 M NaCl, 20mM Tris | |||||||||||||||
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.1 M NaCl, 20mM Tris | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Temp: 113 K / Method: Blot for 2 seconds before plunging Time resolved state: Vitrified 1 hour after mixing DAF with EV7 |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Jan 1, 2000 Details: Micrographs were digitized with a Zeiss PHODIS microdensitometer at 7-micron intervals. |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3670 nm / Nominal defocus min: 1120 nm / Camera length: 0 mm |
Specimen holder | Specimen holder model: OTHER Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder. Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each particle | ||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||
3D reconstruction | Method: common lines fourier method / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 11430 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building |
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Atomic model building | Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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