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Yorodumi- PDB-9emj: SARS-CoV-2 methyltransferase nsp10-16 in complex with Toyocamycin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9emj | ||||||
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Title | SARS-CoV-2 methyltransferase nsp10-16 in complex with Toyocamycin and m7GpppA (Cap0-analog) | ||||||
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Kremling, V. / Sprenger, J. / Oberthuer, D. / Kiene, A. | ||||||
Funding support | 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. / Sprenger, J. / Oberthuer, D. / Chapman, H.N. / Middendorf, P. / Fernandez-Garcia, Y. / Ehrt, C. / Falke, S. / Kiene, A. / Klopprogge, B. / Scheer, T.E.S. / Rarey, M. / ...Authors: Kremling, V. / Sprenger, J. / Oberthuer, D. / Chapman, H.N. / Middendorf, P. / Fernandez-Garcia, Y. / Ehrt, C. / Falke, S. / Kiene, A. / Klopprogge, B. / Scheer, T.E.S. / Rarey, M. / Barthels, F. / Kuehn, S. / Guenther, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9emj.cif.gz | 211.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9emj.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 9emj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/9emj ftp://data.pdbj.org/pub/pdb/validation_reports/em/9emj | HTTPS FTP |
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-Related structure data
Related structure data | 8s8wC 8s8xC 9emlC 9emvC 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: 33912.797 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 |
-Non-polymers , 6 types, 372 molecules
#3: Chemical | ChemComp-TO1 / | ||||
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#4: Chemical | ChemComp-GTA / | ||||
#5: Chemical | ChemComp-MGP / | ||||
#6: Chemical | #7: Chemical | #8: 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 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 |
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-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: 1.03321 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→44.42 Å / Num. obs: 79674 / % possible obs: 99.2 % / Redundancy: 11.8 % / Biso Wilson estimate: 31.54 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1703 / Rpim(I) all: 0.05143 / Rrim(I) all: 0.178 / Net I/σ(I): 9.22 |
Reflection shell | Resolution: 1.79→1.854 Å / Redundancy: 12.1 % / Rmerge(I) obs: 2.292 / Num. unique obs: 7889 / CC1/2: 0.427 / CC star: 0.773 / Rpim(I) all: 0.6777 / Rrim(I) all: 2.391 / % possible all: 98.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→44.42 Å / SU ML: 0.3116 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6709 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: 36.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→44.42 Å
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Refine LS restraints |
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LS refinement shell |
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