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Yorodumi- PDB-7xc3: Crystal structure of SARS-CoV-2 NSP3 Macrodomain 3 (SARS-unique d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xc3 | ||||||
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Title | Crystal structure of SARS-CoV-2 NSP3 Macrodomain 3 (SARS-unique domain-M) | ||||||
Components | Papain-like protease nsp3 | ||||||
Keywords | VIRAL PROTEIN / G-quadruplex-binding macrodomain / SARS-unique domain | ||||||
Function / homology | Function and homology information viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / methylation / double membrane vesicle viral factory outer membrane ...viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / methylation / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / 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 / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion 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 | Li, J. / Gao, J. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Two Binding Sites of SARS-CoV-2 Macrodomain 3 Probed by Oxaprozin and Meclomen. Authors: Li, J. / Zhong, F. / Li, M. / Liu, Y. / Wang, L. / Liu, M. / Li, F. / Zhang, J. / Wu, J. / Shi, Y. / Zhang, Z. / Tu, X. / Ruan, K. / Gao, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xc3.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xc3.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/7xc3 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/7xc3 | HTTPS FTP |
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-Related structure data
Related structure data | 7xc4C 2w2gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14242.358 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Water | ChemComp-HOH / | |
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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: 2.91 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 3.5 M sodium formate, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→56.99 Å / Num. obs: 36862 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.7→1.761 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 12 / Num. unique obs: 3661 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W2G Resolution: 1.7→56.99 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.48 / Stereochemistry target values: ML
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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 max: 49.51 Å2 / Biso mean: 18.7735 Å2 / Biso min: 8.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→56.99 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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