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Yorodumi- PDB-7jir: The crystal structure of Papain-Like Protease of SARS CoV-2 , C11... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jir | |||||||||
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Title | The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457 inhibitor | |||||||||
Components | Papain-like protease | |||||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / covid-19 / coronavirus / SARS / CoV-2 / papain-like protease / IDP51000 / Center for Structural Genomics of Infectious Diseases / CSGID / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex | |||||||||
Function / homology | Function and homology information viral genome replication / methyltransferase activity / 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 ...viral genome replication / methyltransferase activity / 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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / methylation / 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 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / 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: 2.09 Å | |||||||||
Authors | Osipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. ...Osipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. / Kathayat, R. / Snyder, S.A. / Dickinson, B.C. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Authors: Osipiuk, J. / Azizi, S.A. / Dvorkin, S. / Endres, M. / Jedrzejczak, R. / Jones, K.A. / Kang, S. / Kathayat, R.S. / Kim, Y. / Lisnyak, V.G. / Maki, S.L. / Nicolaescu, V. / Taylor, C.A. / ...Authors: Osipiuk, J. / Azizi, S.A. / Dvorkin, S. / Endres, M. / Jedrzejczak, R. / Jones, K.A. / Kang, S. / Kathayat, R.S. / Kim, Y. / Lisnyak, V.G. / Maki, S.L. / Nicolaescu, V. / Taylor, C.A. / Tesar, C. / Zhang, Y.A. / Zhou, Z. / Randall, G. / Michalska, K. / Snyder, S.A. / Dickinson, B.C. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jir.cif.gz | 148.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jir.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 7jir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jir_validation.pdf.gz | 814.6 KB | Display | wwPDB validaton report |
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Full document | 7jir_full_validation.pdf.gz | 816.6 KB | Display | |
Data in XML | 7jir_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 7jir_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/7jir ftp://data.pdbj.org/pub/pdb/validation_reports/ji/7jir | HTTPS FTP |
-Related structure data
Related structure data | 6wrhSC 6wzuC 6xg3C 7jitC 7jivC 7jiwC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35927.695 Da / Num. of mol.: 1 / Mutation: C111S Source method: isolated from a genetically manipulated source Details: 3 N-terminal residues (SNA) are from expression tag Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTC1, UniProt: P0DTD1*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Non-polymers , 6 types, 150 molecules
#2: Chemical | ChemComp-TTT / | ||||||||
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#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Details
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: 4.95 Å3/Da / Density % sol: 75.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder457 |
-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: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 16, 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: 2.09→49.65 Å / Num. obs: 42950 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 51.8 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.042 / Χ2: 1.386 / Net I/av σ(I): 21 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.09→2.13 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 2097 / CC1/2: 0.512 / CC star: 0.823 / Rpim(I) all: 0.592 / Χ2: 0.745 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WRH Resolution: 2.09→49.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.968 / SU B: 8.119 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.63 Å2 / Biso mean: 62.681 Å2 / Biso min: 39.56 Å2
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Refinement step | Cycle: final / Resolution: 2.09→49.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.142 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 49.1789 Å / Origin y: 37.8874 Å / Origin z: 14.483 Å
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