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Yorodumi- PDB-7d6h: Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d6h | |||||||||
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Title | Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant | |||||||||
Components | Papain-like protease | |||||||||
Keywords | HYDROLASE / Protease / Deubiquitinase / VIRAL PROTEIN | |||||||||
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: 1.6 Å | |||||||||
Authors | Liu, J. / Wang, Y. / Pan, L. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Chem Biol / Year: 2021 Title: Development of potent and selective inhibitors targeting the papain-like protease of SARS-CoV-2. Authors: Shan, H. / Liu, J. / Shen, J. / Dai, J. / Xu, G. / Lu, K. / Han, C. / Wang, Y. / Xu, X. / Tong, Y. / Xiang, H. / Ai, Z. / Zhuang, G. / Hu, J. / Zhang, Z. / Li, Y. / Pan, L. / Tan, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d6h.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d6h.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 7d6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/7d6h ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d6h | HTTPS FTP |
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-Related structure data
Related structure data | 7e35C 6w9cS 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: 36110.926 Da / Num. of mol.: 1 / Mutation: C112S 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M acetate buffer pH 4.5, 0.8 M NaH2PO4/1.2M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→49.04 Å / Num. obs: 71014 / % possible obs: 99.99 % / Redundancy: 19.4 % / Biso Wilson estimate: 25.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.018 / Rrim(I) all: 0.08 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.953 / Num. unique obs: 3508 / CC1/2: 0.913 / Rpim(I) all: 0.215 / Rrim(I) all: 0.977 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W9C Resolution: 1.6→27.1 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.52 / 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: 96.46 Å2 / Biso mean: 30.3889 Å2 / Biso min: 18.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→27.1 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25 / % reflection obs: 100 %
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