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Yorodumi- PDB-3epd: CryoEM structure of poliovirus receptor bound to poliovirus type 3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3epd | ||||||
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Title | CryoEM structure of poliovirus receptor bound to poliovirus type 3 | ||||||
Components |
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Keywords | VIRUS / CD155 structure Immunoglobulin Superfamily / poliovirus capsid jelly role / Cell adhesion / Cell membrane / Glycoprotein / Host-virus interaction / Immunoglobulin domain / Membrane / Receptor / Secreted / Transmembrane / VIRAL PROTEIN | ||||||
Function / homology | Function and homology information susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / : / caveolin-mediated endocytosis of virus by host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / RNA-protein covalent cross-linking / positive regulation of natural killer cell mediated cytotoxicity / : / : ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / : / caveolin-mediated endocytosis of virus by host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / RNA-protein covalent cross-linking / positive regulation of natural killer cell mediated cytotoxicity / : / : / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / host cell membrane / cell adhesion molecule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / adherens junction / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / viral capsid / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / signaling receptor activity / DNA replication / host cell cytoplasm / RNA helicase activity / hydrolase activity / symbiont entry into host cell / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular space / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human poliovirus 3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 9 Å | ||||||
Authors | Zhang, P. / Mueller, S. / Morais, M.C. / Bator, C.M. / Bowman, V.D. / Hafenstein, S. / Wimmer, E. / Rossmann, M.G. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2008 Title: Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses. Authors: Ping Zhang / Steffen Mueller / Marc C Morais / Carol M Bator / Valorie D Bowman / Susan Hafenstein / Eckard Wimmer / Michael G Rossmann / Abstract: When poliovirus (PV) recognizes its receptor, CD155, the virus changes from a 160S to a 135S particle before releasing its genome into the cytoplasm. CD155 is a transmembrane protein with 3 Ig-like ...When poliovirus (PV) recognizes its receptor, CD155, the virus changes from a 160S to a 135S particle before releasing its genome into the cytoplasm. CD155 is a transmembrane protein with 3 Ig-like extracellular domains, D1-D3, where D1 is recognized by the virus. The crystal structure of D1D2 has been determined to 3.5-A resolution and fitted into approximately 8.5-A resolution cryoelectron microscopy reconstructions of the virus-receptor complexes for the 3 PV serotypes. These structures show that, compared with human rhinoviruses, the virus-receptor interactions for PVs have a greater dependence on hydrophobic interactions, as might be required for a virus that can inhabit environments of different pH. The pocket factor was shown to remain in the virus during the first recognition stage. The present structures, when combined with earlier mutational investigations, show that in the subsequent entry stage the receptor moves further into the canyon when at a physiological temperature, thereby expelling the pocket factor and separating the viral subunits to form 135S particles. These results provide a detailed analysis of how a nonenveloped virus can enter its host cell. | ||||||
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 | 3epd.cif.gz | 220.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3epd.ent.gz | 171.2 KB | Display | PDB format |
PDBx/mmJSON format | 3epd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3epd_validation.pdf.gz | 905.6 KB | Display | wwPDB validaton report |
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Full document | 3epd_full_validation.pdf.gz | 943.8 KB | Display | |
Data in XML | 3epd_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 3epd_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/3epd ftp://data.pdbj.org/pub/pdb/validation_reports/ep/3epd | HTTPS FTP |
-Related structure data
Related structure data | 1562MC 1563C 1570C 3epcC 3epfC 3uroC 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 R1243
#1: Protein | Mass: 23330.514 Da / Num. of mol.: 1 / Fragment: Poliovirus receptor CD155 D1D2 / Mutation: N105D, N120S, N188Q, N218Q, N237S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PVR, PVS / Production host: Escherichia coli (E. coli) / References: UniProt: P15151 |
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#3: Protein | Mass: 31358.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8B3S0, UniProt: A0A0B6VQW0*PLUS |
#4: Protein | Mass: 29643.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8B3S0, UniProt: P03302*PLUS |
#5: Protein | Mass: 7320.917 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8B3S0, UniProt: P03302*PLUS |
#6: Protein | Mass: 25950.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8B3S0, UniProt: A0A0B4MVN6*PLUS |
-Protein/peptide , 1 types, 1 molecules 0
#2: Protein/peptide | Mass: 446.495 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 2 types, 2 molecules
#7: Chemical | ChemComp-SPH / |
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#8: Chemical | ChemComp-MYR / |
-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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Buffer solution | pH: 7.5 / Details: 10mM Tris-HCl, 20mM NaCl | ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES | ||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T |
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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 magnification: 47000 X / Nominal defocus max: 2749 nm / Nominal defocus min: 985 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software | Name: EMfit / Category: model fitting | ||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 9 Å / Nominal pixel size: 2.69 Å / Actual pixel size: 2.64 Å / Symmetry type: POINT | ||||||||||||
Atomic model building | Space: REAL | ||||||||||||
Refinement step | Cycle: LAST
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