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Yorodumi- PDB-5sok: PanDDA analysis group deposition -- Crystal structure of SARS-CoV... -
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-Basic information
Entry | Database: PDB / ID: 5sok | ||||||
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Title | PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000302059710 - (R) isomer | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | VIRAL PROTEIN / Macrodomain / ADP-ribose / SARS-CoV-2 | ||||||
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 / molecular replacement / Resolution: 1.05 Å | ||||||
Authors | Correy, G.J. / Fraser, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Authors: Gahbauer, S. / Correy, G.J. / Schuller, M. / Ferla, M.P. / Doruk, Y.U. / Rachman, M. / Wu, T. / Diolaiti, M. / Wang, S. / Neitz, R.J. / Fearon, D. / Radchenko, D.S. / Moroz, Y.S. / Irwin, J. ...Authors: Gahbauer, S. / Correy, G.J. / Schuller, M. / Ferla, M.P. / Doruk, Y.U. / Rachman, M. / Wu, T. / Diolaiti, M. / Wang, S. / Neitz, R.J. / Fearon, D. / Radchenko, D.S. / Moroz, Y.S. / Irwin, J.J. / Renslo, A.R. / Taylor, J.C. / Gestwicki, J.E. / von Delft, F. / Ashworth, A. / Ahel, I. / Shoichet, B.K. / Fraser, J.S. #1: Journal: Biorxiv / Year: 2022 Title: Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2. Authors: Gahbauer, S. / Correy, G.J. / Schuller, M. / Ferla, M.P. / Doruk, Y.U. / Rachman, M. / Wu, T. / Diolaiti, M. / Wang, S. / Neitz, R.J. / Fearon, D. / Radchenko, D. / Moroz, Y. / Irwin, J.J. / ...Authors: Gahbauer, S. / Correy, G.J. / Schuller, M. / Ferla, M.P. / Doruk, Y.U. / Rachman, M. / Wu, T. / Diolaiti, M. / Wang, S. / Neitz, R.J. / Fearon, D. / Radchenko, D. / Moroz, Y. / Irwin, J.J. / Renslo, A.R. / Taylor, J.C. / Gestwicki, J.E. / von Delft, F. / Ashworth, A. / Ahel, I. / Shoichet, B.K. / Fraser, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sok.cif.gz | 247.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sok.ent.gz | 205.3 KB | Display | PDB format |
PDBx/mmJSON format | 5sok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5sok_validation.pdf.gz | 757.1 KB | Display | wwPDB validaton report |
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Full document | 5sok_full_validation.pdf.gz | 759.8 KB | Display | |
Data in XML | 5sok_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5sok_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/5sok ftp://data.pdbj.org/pub/pdb/validation_reports/so/5sok | HTTPS FTP |
-Group deposition
ID | G_1002236 (50 entries) |
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Title | PanDDA analysis group deposition of SARS-CoV-2 NSP3 macrodomain ligand screen |
Type | changed state |
Description | SARS-CoV-2 NSP3 macrodomain in complex with ligands identified by X-ray diffraction using ALS 8.3.1, SSRL 12-1 and 12-2, and NSLS-II 17-ID-2 |
-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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18178.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HIS6 purification tag and linker (MHHHHHHSSGVDLGTENLYFQ) cleaved with TEV protease Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-RVO / | #3: 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: 2.13 Å3/Da / Density % sol: 42.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 100 mM CHES, 28% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.88557 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.88557 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→39.67 Å / Num. obs: 142528 / % possible obs: 99.8 % / Redundancy: 6.44 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.083 / Χ2: 0.734 / Net I/σ(I): 9.68 / Num. measured all: 917843 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→39.67 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.9 / Stereochemistry target values: ML
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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 max: 56.35 Å2 / Biso mean: 19.0839 Å2 / Biso min: 8.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.05→39.67 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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