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Yorodumi- PDB-4rs5: Crystal structure of an uncoating intermediate of a EV71 recombin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rs5 | ||||||
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Title | Crystal structure of an uncoating intermediate of a EV71 recombinant virus | ||||||
Components |
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Keywords | VIRUS / eight-stranded beta barrel / replicate in cytoplasm | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterovirus A71 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.805 Å | ||||||
Authors | Chen, R. / Lyu, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Crystal structures of enterovirus 71 (EV71) recombinant virus particles provide insights into vaccine design. Authors: Lyu, K. / Wang, G.C. / He, Y.L. / Han, J.F. / Ye, Q. / Qin, C.F. / Chen, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rs5.cif.gz | 661.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rs5.ent.gz | 538.5 KB | Display | PDB format |
PDBx/mmJSON format | 4rs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/4rs5 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/4rs5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a 60mer generated from the pentamer in the asymmetric unit by the following 12 operations: (x,y,z),(-x,-y,z),(-x,y,-z),(x,-y,-z),(y,z,x),(-y,-z,x),(-y,z,-x),(y,-z,-x),(z,x,y),(-z,-x,y),(-z,x,-y) and (z,-x,-y). The pentamer in the asymmetric unit is generated from the deposited PDB by the following transformations(r11,r12,r13,r21,r22,r23,r31,r32,r33,tx,tx,tz):(1,0,0,0,1,0,0,0,1,0,0,0), (-0.8127, 0.5018, -0.2962, -0.4896, -0.3124, 0.8141, 0.316, 0.8066, 0.4996, 1.955, 0.5457, -0.138), (0.3088, 0.809, -0.5002, -0.8085, 0.5003, 0.3099, 0.501, 0.3087, 0.8086, -0.07626, 0.23, -0.006095), (-0.8092, -0.4849, 0.3318, 0.5077, -0.2928, 0.8103, -0.2957, 0.8241, 0.4831, 4.346, 1.46, -1.11) and (0.2998, -0.8038, 0.5138, 0.803, 0.5034, 0.319, -0.515, 0.3169, 0.7964, 2.491, 1.66, -0.7237). |
-Components
#1: Protein | Mass: 26440.148 Da / Num. of mol.: 5 / Mutation: K550Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Cell line (production host): RD cells / Production host: Homo sapiens (human) / References: UniProt: F6KTB0 #2: Protein | Mass: 35209.219 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Cell line (production host): RD cells / Production host: Homo sapiens (human) / References: UniProt: F6KTB0 #3: Protein | Mass: 34369.754 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Cell line (production host): RD cells / Production host: Homo sapiens (human) / References: UniProt: F6KTB0 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 66.99 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M MES containing 1.6M sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.281579 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2013 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.281579 Å / Relative weight: 1 |
Reflection | Resolution: 3.805→46.791 Å / Num. all: 119163 / Num. obs: 97564 / % possible obs: 81.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.8→3.94 Å / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.805→46.791 Å / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.805→46.791 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→3.9 Å
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