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- PDB-3epf: CryoEM structure of poliovirus receptor bound to poliovirus type 2 -
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Basic information
Entry | Database: PDB / ID: 3epf | ||||||
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Title | CryoEM structure of poliovirus receptor bound to poliovirus type 2 | ||||||
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![]() | 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 | ![]() susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of mast cell activation / regulation of viral entry into host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / acrosome assembly ...susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of mast cell activation / regulation of viral entry into host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / acrosome assembly / positive regulation of natural killer cell mediated cytotoxicity / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of T cell receptor signaling pathway / 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 / cell adhesion molecule binding / cytoskeleton organization / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / host cell cytoplasmic vesicle membrane / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / signaling receptor activity / symbiont-mediated suppression of host gene expression / DNA replication / receptor-mediated endocytosis of virus by host cell / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / fusion of virus membrane with host plasma membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | ||||||
![]() | Zhang, P. / Mueller, S. / Morais, M.C. / Bator, C.M. / Bowman, V.D. / Hafenstein, S. / Wimmer, E. / Rossmann, M.G. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.2 KB | Display | ![]() |
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PDB format | ![]() | 174.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 928.8 KB | Display | ![]() |
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Full document | ![]() | 968.5 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 59.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1563MC ![]() 1562C ![]() 1570C ![]() 3epcC ![]() 3epdC ![]() 3uroC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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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.) ![]() ![]() ![]() |
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#2: Protein | Mass: 30734.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 29045.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 7346.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 26115.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 273 molecules ![](data/chem/img/SC4.gif)
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#6: Chemical | ChemComp-SC4 / |
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#7: Chemical | ChemComp-MYR / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 7.5 / Details: 10mM Tris-HCl, 20mM NaCl | ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 2745 nm / Nominal defocus min: 1236 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
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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: 2.66 Å / Symmetry type: POINT | ||||||||||||
Atomic model building | Space: REAL | ||||||||||||
Refinement step | Cycle: LAST
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