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Yorodumi- PDB-7d3i: Crystal structure of SARS-CoV-2 main protease in complex with MI-23 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d3i | ||||||
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Title | Crystal structure of SARS-CoV-2 main protease in complex with MI-23 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / coronavirus / protease / inhibitor / complex / VIRAL PROTEIN. | ||||||
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 / 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 ...viral genome replication / methyltransferase activity / 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 / methylation / 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 / endonuclease 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: 2.004 Å | ||||||
Authors | Zeng, R. / Li, Y.S. / Qiao, J.X. / Wang, Y.F. / Yang, S.Y. / Lei, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Science / Year: 2021 Title: SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model. Authors: Qiao, J. / Li, Y.S. / Zeng, R. / Liu, F.L. / Luo, R.H. / Huang, C. / Wang, Y.F. / Zhang, J. / Quan, B. / Shen, C. / Mao, X. / Liu, X. / Sun, W. / Yang, W. / Ni, X. / Wang, K. / Xu, L. / ...Authors: Qiao, J. / Li, Y.S. / Zeng, R. / Liu, F.L. / Luo, R.H. / Huang, C. / Wang, Y.F. / Zhang, J. / Quan, B. / Shen, C. / Mao, X. / Liu, X. / Sun, W. / Yang, W. / Ni, X. / Wang, K. / Xu, L. / Duan, Z.L. / Zou, Q.C. / Zhang, H.L. / Qu, W. / Long, Y.H. / Li, M.H. / Yang, R.C. / Liu, X. / You, J. / Zhou, Y. / Yao, R. / Li, W.P. / Liu, J.M. / Chen, P. / Liu, Y. / Lin, G.F. / Yang, X. / Zou, J. / Li, L. / Hu, Y. / Lu, G.W. / Li, W.M. / Wei, Y.Q. / Zheng, Y.T. / Lei, J. / Yang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d3i.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d3i.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 7d3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/7d3i ftp://data.pdbj.org/pub/pdb/validation_reports/d3/7d3i | HTTPS FTP |
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-Related structure data
Related structure data | 7c7pSC 7comC 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: 33825.547 Da / Num. of mol.: 1 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, UniProt: P0DTD1*PLUS, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-GQU / ( |
#3: Chemical | ChemComp-TRS / |
#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: 1.9 Å3/Da / Density % sol: 35.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1% w/v n-octyl-beta-D-glucoside, 0.1 M sodium citrate tribasic dihydrate pH 5.5, 22% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.38 Å / Num. obs: 17469 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2→2.06 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1217 / CC1/2: 0.888 / Rpim(I) all: 0.213 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C7P Resolution: 2.004→47.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.164
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Displacement parameters | Biso max: 113.12 Å2 / Biso mean: 34.73 Å2 / Biso min: 18.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.004→47.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.004→2.02 Å / Rfactor Rfree error: 0
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