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Yorodumi- PDB-6wcf: Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wcf | ||||||
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Title | Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in complex with MES | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | HYDROLASE / SARS Coronavirus / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN | ||||||
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: 1.065 Å | ||||||
Authors | Michalska, K. / Kim, Y. / Jedrzejczak, R. / Maltseva, N. / Endres, M. / Mesecar, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Iucrj / Year: 2020 Title: Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes. Authors: Michalska, K. / Kim, Y. / Jedrzejczak, R. / Maltseva, N.I. / Stols, L. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wcf.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wcf.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 6wcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/6wcf ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wcf | HTTPS FTP |
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-Related structure data
Related structure data | 6vxsC 6w02C 6w6ySC 6wenC S: Starting model for refinement C: citing same article (ref.) |
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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: 18275.771 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 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.52 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, PH 6.5, 30% W/V PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 24, 2020 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.065→50 Å / Num. obs: 64283 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 10 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.74 |
Reflection shell | Resolution: 1.065→1.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 3077 / CC1/2: 0.564 / CC star: 0.849 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W6Y Resolution: 1.065→33.13 Å / SU ML: 0.0784 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.4149 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.065→33.13 Å
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Refine LS restraints |
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LS refinement shell |
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