+Open data
-Basic information
Entry | Database: PDB / ID: 3sjk | ||||||
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Title | Crystal structure of the C147A mutant 3C from enterovirus 71 | ||||||
Components |
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Keywords | HYDROLASE / chymotrypsin-like fold / protease | ||||||
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 / nucleoside-triphosphate phosphatase ...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 / symbiont-mediated suppression of host gene expression / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 | Human enterovirus 71 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.096 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 | 3sjk.cif.gz | 87.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sjk.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 3sjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sjk_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 3sjk_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 3sjk_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3sjk_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/3sjk ftp://data.pdbj.org/pub/pdb/validation_reports/sj/3sjk | HTTPS FTP |
-Related structure data
Related structure data | 3sj8SC 3sj9C 3sjiC 3sjoC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21117.145 Da / Num. of mol.: 1 / Fragment: UNP residues 1549-1731 / Mutation: C147A 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, UniProt: F6KTB0*PLUS, picornain 3C |
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#2: Protein/peptide | Mass: 785.974 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS STATE THAT CHAIN B (PEPTIDE KPVLRTATVQ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 20 mM lithium sulfate, 25% w/v PEG5000 MME, 8 mM 16-mer peptide, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 26, 2010 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.096→50 Å / Num. all: 12411 / Num. obs: 12238 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17.871 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.184 / Num. unique all: 1150 / Rsym value: 0.477 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SJ8 Resolution: 2.096→17.573 Å / SU ML: 0.28 / σ(F): 0.14 / Phase error: 23.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.252 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.096→17.573 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: 14.8545 Å / Origin y: 18.9285 Å / Origin z: 0.6461 Å
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Refinement TLS group | Selection details: all |