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Yorodumi- PDB-7u29: Structure of SARS-CoV-2 Mpro mutant (K90R) in complex with Nirmat... -
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-Basic information
Entry | Database: PDB / ID: 7u29 | ||||||
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Title | Structure of SARS-CoV-2 Mpro mutant (K90R) in complex with Nirmatrelvir (PF-07321332) | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Protease / SARS-CoV-2 / covalent complex / inhibitor / HYDROLASE-INHIBITOR complex / Omicron / nirmatrelvir / PF-07321332 / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.088 Å | ||||||
Authors | Greasley, S.E. / Ferre, R.A. / Liu, W. / Stewart, A.E. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. Authors: Greasley, S.E. / Noell, S. / Plotnikova, O. / Ferre, R. / Liu, W. / Bolanos, B. / Fennell, K. / Nicki, J. / Craig, T. / Zhu, Y. / Stewart, A.E. / Steppan, C.M. #1: Journal: Biorxiv / Year: 2022 Title: Structural basis for Nirmatrelvir in vitro efficacy against the Omicron variant of SARS-CoV-2 Authors: Greasley, S.E. / Noell, S. / Plotnikova, O. / Ferre, R. / Liu, W. / Bolanos, B. / Fennell, K. / Nicki, J. / Craig, T. / Zhu, Y. / Stewart, A.E. / Steppan, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u29.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u29.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 7u29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/7u29 ftp://data.pdbj.org/pub/pdb/validation_reports/u2/7u29 | HTTPS FTP |
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-Related 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: 33853.559 Da / Num. of mol.: 2 / Mutation: K90R 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: 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: 2.07 Å3/Da / Density % sol: 40.49 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 20.0 %w/v PEG 3350 and 0.2071428571 M sodium sulfate decahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 6, 2022 |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→110.22 Å / Num. obs: 28383 / % possible obs: 85.7 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.075 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1419 / CC1/2: 0.583 / Rpim(I) all: 0.499 / % possible all: 40.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.088→110.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.243
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Displacement parameters | Biso mean: 30.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.088→110.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.14 Å
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