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Yorodumi- PDB-8gqc: Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gqc | ||||||
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Title | Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.35 angstrom resolution) | ||||||
Components | Papain-like protease nsp3 | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / NSP3 / SUD domain / G4-binding / virus replication / drug target | ||||||
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: 1.35 Å | ||||||
Authors | Qin, B. / Li, Z. / Aumonier, S. / Wang, M. / Cui, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Identification of the SARS-unique domain of SARS-CoV-2 as an antiviral target. Authors: Qin, B. / Li, Z. / Tang, K. / Wang, T. / Xie, Y. / Aumonier, S. / Wang, M. / Yuan, S. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gqc.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqc.ent.gz | 132.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqc ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqc | HTTPS FTP |
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-Related structure data
Related structure data | 8hblC 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: 29022.396 Da / Num. of mol.: 1 / Fragment: SUD domain / Mutation: L492C, Y623C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.20 M Lithium sulfate monohydrate, 0.10 M Tris pH= 8.50, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 274 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99995 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99995 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→37.85 Å / Num. obs: 55560 / % possible obs: 96 % / Observed criterion σ(I): 1.2 / Redundancy: 20 % / Biso Wilson estimate: 22.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.01 / Net I/av σ(I): 30.5 / Net I/σ(I): 1.2 |
Reflection shell | Resolution: 1.351→1.485 Å / Redundancy: 19.4 % / Rmerge(I) obs: 1.733 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 53798 / CC1/2: 0.693 / Rpim(I) all: 0.403 / % possible all: 72.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2w2g Resolution: 1.35→37.85 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.08 / 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: 101.18 Å2 / Biso mean: 33.8542 Å2 / Biso min: 15.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→37.85 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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