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Yorodumi- PDB-8s8x: SARS-CoV-2 nsp10-16 methyltransferase in complex with Toyocamycin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8s8x | ||||||
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Title | SARS-CoV-2 nsp10-16 methyltransferase in complex with Toyocamycin and m7GpppA-RNA (Cap0-RNA) | ||||||
Components |
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Keywords | VIRAL PROTEIN / methyltransferase / complex / inhibitor | ||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / copper ion binding / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Kremling, V. / Sprenger, J. / Oberthuer, D. / Scheer, T.E.S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug development Authors: Kremling, V. / Falke, S. / Fernandez-Garcia, Y. / Ehrt, C. / Kiene, A. / Klopprogge, B. / Scheer, T.E.S. / Barthels, F. / Middendorf, P. / Kuehn, S. / Guenther, S. / Rarey, M. / Chapman, H.N. ...Authors: Kremling, V. / Falke, S. / Fernandez-Garcia, Y. / Ehrt, C. / Kiene, A. / Klopprogge, B. / Scheer, T.E.S. / Barthels, F. / Middendorf, P. / Kuehn, S. / Guenther, S. / Rarey, M. / Chapman, H.N. / Oberthuer, D. / Sprenger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s8x.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s8x.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 8s8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s8x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8s8x_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8s8x_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 8s8x_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/8s8x ftp://data.pdbj.org/pub/pdb/validation_reports/s8/8s8x | HTTPS FTP |
-Related structure data
Related structure data | 8s8wC 9emjC 9emlC 9emvC 9eunC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 34150.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1, methyltransferase cap1 |
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#2: Protein | Mass: 14859.983 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1 |
-RNA chain , 1 types, 1 molecules C
#3: RNA chain | Mass: 896.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 6 types, 255 molecules
#4: Chemical | ChemComp-MES / | ||||
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#5: Chemical | ChemComp-TO1 / | ||||
#6: Chemical | ChemComp-MG / | ||||
#7: Chemical | #8: Chemical | ChemComp-GTA / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 4.22 Å3/Da / Density % sol: 70.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 400 mM sodium fluoride, 100 mM 2-(N-morpholino)ethanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→49.06 Å / Num. obs: 113051 / % possible obs: 97.47 % / Redundancy: 11.9 % / Biso Wilson estimate: 45.88 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.3314 / Rpim(I) all: 0.09984 / Rrim(I) all: 0.3462 / Net I/σ(I): 4.64 |
Reflection shell | Resolution: 1.99→2.1 Å / Redundancy: 12 % / Rmerge(I) obs: 3.205 / Mean I/σ(I) obs: 0.14 / Num. unique obs: 16215 / CC1/2: 0.271 / CC star: 0.653 / Rpim(I) all: 0.9586 / Rrim(I) all: 3.346 / % possible all: 82.31 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→49.06 Å / SU ML: 0.3339 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 26.1455 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→49.06 Å
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Refine LS restraints |
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LS refinement shell |
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