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Yorodumi- PDB-7en8: Crystal structure of SARS-CoV-2 3CLpro in complex with the non-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7en8 | ||||||
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Title | Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-04 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / Non-covalent / Inhibitor / 3CLpro / Coronavirus | ||||||
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 / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...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 / 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 / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / 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 / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral translational frameshifting / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Hou, N. / Peng, C. / Hu, Q. | ||||||
Citation | Journal: Acs Cent.Sci. / Year: 2023 Title: Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro. Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / ...Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / Zou, J. / Schindewolf, C. / Menachery, V. / Su, W. / Yuan, Y. / Shen, Z. / Zhang, R. / Yuan, S. / Yu, H. / Shi, P.Y. / Bu, Z. / Huang, J. / Hu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7en8.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7en8.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 7en8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7en8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7en8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7en8_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 7en8_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/7en8 ftp://data.pdbj.org/pub/pdb/validation_reports/en/7en8 | HTTPS FTP |
-Related structure data
Related structure data | 7en9C 7endC 7eneC 6y2eS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 1 - 301 / Label seq-ID: 1 - 301
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-Components
#1: Protein | Mass: 33825.547 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 (E. coli) References: UniProt: P0DTC1, SARS coronavirus main proteinase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | 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: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.5% v/v Tacsimate pH 4.0, 0.1 M sodium acetate trihydrate pH 4.6, 20% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.541 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→29 Å / Num. obs: 55659 / % possible obs: 99.27 % / Redundancy: 4 % / Biso Wilson estimate: 13.76 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.0677 / Rrim(I) all: 0.1428 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.83→1.895 Å / Rmerge(I) obs: 0.3773 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 5444 / CC1/2: 0.861 / Rpim(I) all: 0.26 / Rrim(I) all: 0.4617 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y2E Resolution: 1.83→29 Å / SU ML: 0.2878 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5563 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 15.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→29 Å
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Refine LS restraints |
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LS refinement shell |
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