+Open data
-Basic information
Entry | Database: PDB / ID: 7kri | ||||||
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Title | FR6-bound SARS-CoV-2 Nsp9 RNA-replicase | ||||||
Components | Non-structural protein 9 | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / Nsp9 / RNA Binding Complex | ||||||
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 / symbiont-mediated suppression of host NF-kappaB cascade / 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 / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / 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 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / viral translational frameshifting / induction by virus of host autophagy / copper ion binding / 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 / 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: 1.58 Å | ||||||
Authors | Littler, D.R. / Gully, B.S. / Rossjohn, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9. Authors: Littler, D.R. / Mohanty, B. / Lowery, S.A. / Colson, R.N. / Gully, B.S. / Perlman, S. / Scanlon, M.J. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kri.cif.gz | 197.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kri.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kri_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7kri_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7kri_validation.xml.gz | 21 KB | Display | |
Data in CIF | 7kri_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/7kri ftp://data.pdbj.org/pub/pdb/validation_reports/kr/7kri | HTTPS FTP |
-Related structure data
Related structure data | 6w9qS S: Starting model for refinement |
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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
#1: Protein | Mass: 14592.642 Da / Num. of mol.: 3 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 (E. coli) / Strain (production host): B / References: UniProt: P0DTD1 #2: Chemical | #3: Chemical | ChemComp-X0Y / #4: Chemical | ChemComp-MLI / | #5: Water | ChemComp-HOH / | 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: 3.1 Å3/Da / Density % sol: 60.31 % / Description: Brown coloured |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4 Details: 0.1M Sodium Citrate pH 4.0 2.2-2.4M Sodium Malonate PH range: 4 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95374 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→44.62 Å / Num. obs: 73088 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 23.15 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 10.5 % / Num. unique obs: 3604 / CC1/2: 0.602 / Rpim(I) all: 0.619 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W9Q Resolution: 1.58→44.62 Å / SU ML: 0.158 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1219 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: 31.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→44.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 55.2200581011 Å / Origin y: -11.3539848896 Å / Origin z: 8.54631795271 Å
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Refinement TLS group | Selection details: all |