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Yorodumi- PDB-8h3l: Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutan... -
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-Basic information
Entry | Database: PDB / ID: 8h3l | ||||||
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Title | Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Enstrelvir | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / Mutant | ||||||
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 / 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 / methylation / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wang, H. / Lin, M. / Duan, Y. / Zhang, X. / Zhou, H. / Bian, Q. / Liu, X. / Rao, Z. / Yang, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2023 Title: Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Authors: Duan, Y. / Zhou, H. / Liu, X. / Iketani, S. / Lin, M. / Zhang, X. / Bian, Q. / Wang, H. / Sun, H. / Hong, S.J. / Culbertson, B. / Mohri, H. / Luck, M.I. / Zhu, Y. / Liu, X. / Lu, Y. / Yang, ...Authors: Duan, Y. / Zhou, H. / Liu, X. / Iketani, S. / Lin, M. / Zhang, X. / Bian, Q. / Wang, H. / Sun, H. / Hong, S.J. / Culbertson, B. / Mohri, H. / Luck, M.I. / Zhu, Y. / Liu, X. / Lu, Y. / Yang, X. / Yang, K. / Sabo, Y. / Chavez, A. / Goff, S.P. / Rao, Z. / Ho, D.D. / Yang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h3l.cif.gz | 247.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h3l.ent.gz | 198.3 KB | Display | PDB format |
PDBx/mmJSON format | 8h3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h3l_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8h3l_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8h3l_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 8h3l_validation.cif.gz | 63.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/8h3l ftp://data.pdbj.org/pub/pdb/validation_reports/h3/8h3l | HTTPS FTP |
-Related structure data
Related structure data | 8h3gC 8h3kC 8h4yC 8h51C 8h57C 8h5fC 8h5pC 8h6iC 8h6nC 8h7kC 8h7wC 8h82C 8hbkC 7vu6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33807.617 Da / Num. of mol.: 4 / Mutation: T21I, E166V 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 | ChemComp-7YY / #3: 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: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 2% v/v Tacsimate pH 7.0, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.978642 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 17, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978642 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→44.64 Å / Num. obs: 49388 / % possible obs: 99.4 % / Redundancy: 5.097 % / Biso Wilson estimate: 38.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.148 / Χ2: 0.711 / Net I/σ(I): 7.55 / Num. measured all: 251742 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VU6 Resolution: 2.3→44.64 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.48 / Phase error: 30.77 / 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: 131.47 Å2 / Biso mean: 42.5572 Å2 / Biso min: 19.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→44.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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