+Open data
-Basic information
Entry | Database: PDB / ID: 7n3k | ||||||
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Title | Oridonin-bound SARS-CoV-2 Nsp9 | ||||||
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 / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Littler, D.R. / Gully, B.S. / Rossjohn, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein. Authors: Littler, D.R. / Liu, M. / McAuley, J.L. / Lowery, S.A. / Illing, P.T. / Gully, B.S. / Purcell, A.W. / Chandrashekaran, I.R. / Perlman, S. / Purcell, D.F.J. / Quinn, R.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 | 7n3k.cif.gz | 412.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n3k.ent.gz | 328.7 KB | Display | PDB format |
PDBx/mmJSON format | 7n3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n3k_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 7n3k_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 7n3k_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 7n3k_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/7n3k ftp://data.pdbj.org/pub/pdb/validation_reports/n3/7n3k | HTTPS FTP |
-Related structure data
Related structure data | 7kriS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14592.642 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pET-28-NKI-LIC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0DTD1 #2: Chemical | ChemComp-ODN / ( #3: Chemical | ChemComp-SO4 / Has ligand of interest | Y | Has protein modification | 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: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% PEG 4000, 0.17M NH4SO4, 0.1M NaCitrate Phosphate pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 3→88.2 Å / Num. obs: 25089 / % possible obs: 99.1 % / Observed criterion σ(I): 1.5 / Redundancy: 3.1 % / Rpim(I) all: 0.035 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3→3.16 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3682 / Rpim(I) all: 0.525 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KRI Resolution: 3→60 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 107 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→60 Å
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Refine LS restraints |
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