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Yorodumi- PDB-8rv8: SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rv8 | ||||||
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Title | SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 5 | ||||||
Components |
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Keywords | VIRAL PROTEIN / nsp16 / nsp10 / 2'-O-methyltransferase | ||||||
Function / homology | Function and homology information viral genome replication / methyltransferase activity / 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 ...viral genome replication / methyltransferase activity / 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 / 5'-3' DNA helicase activity / 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 endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / 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 / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / virus-mediated perturbation of host defense response / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / 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: 1.7 Å | ||||||
Authors | Kalnins, G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 5 Authors: Kalnins, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rv8.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rv8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/8rv8 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rv8 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 33701.645 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: 15078.259 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC1 |
-Non-polymers , 5 types, 304 molecules
#3: Chemical | ChemComp-MES / | ||||
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#4: Chemical | ChemComp-A1H28 / Mass: 437.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16ClN5O5S / Feature type: SUBJECT OF INVESTIGATION | ||||
#5: Chemical | #6: Chemical | #7: 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 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M MES (pH 5.6), 11% PEG 3350, 0.24 M magnesium chloride |
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-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.08 Å / Num. obs: 92755 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 26.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.021 / Rrim(I) all: 0.097 / Χ2: 1 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 21 % / Rmerge(I) obs: 2.739 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 95651 / CC1/2: 0.509 / Rpim(I) all: 0.628 / Rrim(I) all: 2.891 / Χ2: 1.01 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.39 Å / SU ML: 0.2033 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5676 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42.39 Å
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Refine LS restraints |
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LS refinement shell |
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