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Yorodumi- PDB-9aum: Structure of SARS-CoV-2 Mpro mutant (T21I,S144A,T304I) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9aum | ||||||
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Title | Structure of SARS-CoV-2 Mpro mutant (T21I,S144A,T304I) in complex with Nirmatrelvir (PF-07321332) | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / protease / SARS-CoV / HYDROLASE-INHIBITOR complex | ||||||
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 / symbiont-mediated suppression of host NF-kappaB cascade / 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 / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / viral translational frameshifting / 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: 1.539 Å | ||||||
Authors | Gajiwala, K.S. / Greasley, S.E. / Ferre, R.A. / Liu, W. / Stewart, A.E. | ||||||
Funding support | 1items
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Citation | Journal: Sci Adv / Year: 2024 Title: In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance. Authors: Zhu, Y. / Yurgelonis, I. / Noell, S. / Yang, Q. / Guan, S. / Li, Z. / Hao, L. / Rothan, H. / Rai, D.K. / McMonagle, P. / Baniecki, M.L. / Greasley, S.E. / Plotnikova, O. / Lee, J. / Nicki, J. ...Authors: Zhu, Y. / Yurgelonis, I. / Noell, S. / Yang, Q. / Guan, S. / Li, Z. / Hao, L. / Rothan, H. / Rai, D.K. / McMonagle, P. / Baniecki, M.L. / Greasley, S.E. / Plotnikova, O. / Lee, J. / Nicki, J.A. / Ferre, R. / Byrnes, L.J. / Liu, W. / Craig, T.K. / Steppan, C.M. / Liberator, P. / Soares, H.D. / Allerton, C.M.N. / Anderson, A.S. / Cardin, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9aum.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9aum.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 9aum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9aum_validation.pdf.gz | 862.7 KB | Display | wwPDB validaton report |
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Full document | 9aum_full_validation.pdf.gz | 863.7 KB | Display | |
Data in XML | 9aum_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 9aum_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/9aum ftp://data.pdbj.org/pub/pdb/validation_reports/au/9aum | HTTPS FTP |
-Related structure data
Related structure data | 9aujC 9aukC 9aulC 9aunC 9auoC 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: 33833.656 Da / Num. of mol.: 1 / Mutation: T21I,S144A,T304I 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-4WI / ( |
#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: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: 0.1 M Tris, pH 8, 20 % 2-propanol, 5 % PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→41.68 Å / Num. obs: 36169 / % possible obs: 78.4 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.54→1.65 Å / Num. unique obs: 1808 / CC1/2: 0.581 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.539→27.29 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.103
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Displacement parameters | Biso mean: 21.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.539→27.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.61 Å
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