+Open data
-Basic information
Entry | Database: PDB / ID: 3sjo | ||||||
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Title | structure of EV71 3C in complex with Rupintrivir (AG7088) | ||||||
Components | 3C proteasePicornain 3C | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / in complex with Rupintrivir / Chymotrypsin-like fold / protease / C147 covalently binds to Rupintrivir / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human enterovirus 71 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å | ||||||
Authors | Lu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F. | ||||||
Citation | Journal: J.Virol. / Year: 2011 Title: Enterovirus 71 and Coxsackievirus A16 3C Proteases: Binding to Rupintrivir and Their Substrates and Anti-Hand, Foot, and Mouth Disease Virus Drug Design. Authors: Lu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sjo.cif.gz | 574 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sjo.ent.gz | 473.9 KB | Display | PDB format |
PDBx/mmJSON format | 3sjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/3sjo ftp://data.pdbj.org/pub/pdb/validation_reports/sj/3sjo | HTTPS FTP |
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-Related structure data
Related structure data | 3sj8SC 3sj9C 3sjiC 3sjkC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21149.209 Da / Num. of mol.: 8 / Fragment: UNP residues 1549-1731 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human enterovirus 71 / Strain: Anhui1-09-China / Gene: 3C / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E0WWC7, picornain 3C #2: Chemical | ChemComp-AG7 / #3: Water | ChemComp-HOH / | |
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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: 1.96 Å3/Da / Density % sol: 37.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, 25% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2011 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 140985 / Num. obs: 136411 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 20.642 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.182 / Num. unique all: 13450 / Rsym value: 0.312 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SJ8 Resolution: 1.702→34.536 Å / σ(F): 0.1 / Phase error: 23.26 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.774 Å2 / ksol: 0.401 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.702→34.536 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -8.7098 Å / Origin y: -9.1947 Å / Origin z: -32.5069 Å
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Refinement TLS group | Selection details: all |