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Yorodumi- PDB-8dd1: SARS-CoV-2 Main Protease (Mpro) H164N Mutant in Complex with Inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dd1 | ||||||
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Title | SARS-CoV-2 Main Protease (Mpro) H164N Mutant in Complex with Inhibitor GC376 | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN / Protease / SARS-CoV-2 / Mpro / Mutation | ||||||
Function / homology | Function and homology information 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 ...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 / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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: 2.03 Å | ||||||
Authors | Lewandowski, E.M. / Butler, S.G. / Hu, Y. / Tan, H. / Wang, J. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2023 Title: Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir. Authors: Hu, Y. / Lewandowski, E.M. / Tan, H. / Zhang, X. / Morgan, R.T. / Zhang, X. / Jacobs, L.M.C. / Butler, S.G. / Gongora, M.V. / Choy, J. / Deng, X. / Chen, Y. / Wang, J. #1: Journal: Biorxiv / Year: 2022 Title: Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir. Authors: Hu, Y. / Lewandowski, E.M. / Tan, H. / Zhang, X. / Morgan, R.T. / Zhang, X. / Jacobs, L.M.C. / Butler, S.G. / Gongora, M.V. / Choy, J. / Deng, X. / Chen, Y. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dd1.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dd1.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dd1_validation.pdf.gz | 776.2 KB | Display | wwPDB validaton report |
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Full document | 8dd1_full_validation.pdf.gz | 777.2 KB | Display | |
Data in XML | 8dd1_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 8dd1_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/8dd1 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/8dd1 | HTTPS FTP |
-Related structure data
Related structure data | 8dczC 8dd9C 8dfeC 8dfnC 8dgbC 7lyhS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33801.500 Da / Num. of mol.: 1 / Mutation: H164N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-K36 / ( |
#3: 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: 2 Å3/Da / Density % sol: 38.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 25 % PEG 3350 , 0.1M Potassium/Sodium Tartrate, 0.0005 M Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 16735 / % possible obs: 97 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 22.18 |
Reflection shell | Resolution: 2.04→2.08 Å / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 863 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LYH Resolution: 2.03→34.24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.442 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.209 / 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: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.41 Å2 / Biso mean: 42.87 Å2 / Biso min: 21.93 Å2
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Refinement step | Cycle: final / Resolution: 2.03→34.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.033→2.086 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.198 Å / Origin y: 0.817 Å / Origin z: 4.46 Å
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