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Yorodumi- PDB-6lse: Crystal structure of the enterovirus 71 polymerase elongation com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lse | ||||||
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Title | Crystal structure of the enterovirus 71 polymerase elongation complex (C3S6A/C3S6B form) | ||||||
Components |
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Keywords | TRANSFERASE/RNA / polymerase-RNA complex / elongation / translocation / TRANSFERASE / TRANSFERASE-RNA 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 / 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 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Wang, M. / Shu, B. / Jing, X. / Gong, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures. Authors: Wang, M. / Li, R. / Shu, B. / Jing, X. / Ye, H.Q. / Gong, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lse.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lse.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/6lse ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6lse | HTTPS FTP |
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-Related structure data
Related structure data | 6lsfC 6lsgC 6lshC 5f8lS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53408.461 Da / Num. of mol.: 1 / Mutation: C291M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human enterovirus 71 / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pCG1 / References: UniProt: E5RPG3, RNA-directed RNA polymerase |
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-RNA chain , 2 types, 2 molecules BC
#2: RNA chain | Mass: 11260.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 6117.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 175 molecules
#4: Chemical | ChemComp-ZN / | ||||
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#5: Chemical | #6: Chemical | ChemComp-POP / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.73 Å3/Da / Density % sol: 58.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.5 / Details: MES, PEG 5000 monomethyl ether, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 32014 / % possible obs: 87.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.04 / Rrim(I) all: 0.092 / Χ2: 0.946 / Net I/σ(I): 8.6 / Num. measured all: 140354 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5f8L Resolution: 2.25→48.58 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.53 Å2 / Biso mean: 45.928 Å2 / Biso min: 25.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→48.58 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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