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Yorodumi- PDB-7t8m: Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t8m | ||||||
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Title | Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 5/6 | ||||||
Components |
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Keywords | VIRAL PROTEIN / Coronavirus / COVID-19 / COVID / PROTEASE / DRUG RESISTANCE / COMPLEX / HYDROLASE / DURG DISCOVERY / MAIN PROTEASE / MPRO / SUBSTRATE COMPLEX / NSP 5/6 | ||||||
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 / 3'-5'-RNA exonuclease activity / 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 / host cell endoplasmic reticulum membrane / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Shaqra, A.M. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Authors: Shaqra, A.M. / Zvornicanin, S.N. / Huang, Q.Y.J. / Lockbaum, G.J. / Knapp, M. / Tandeske, L. / Bakan, D.T. / Flynn, J. / Bolon, D.N.A. / Moquin, S. / Dovala, D. / Kurt Yilmaz, N. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t8m.cif.gz | 187.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t8m.ent.gz | 118 KB | Display | PDB format |
PDBx/mmJSON format | 7t8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t8m_validation.pdf.gz | 481.8 KB | Display | wwPDB validaton report |
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Full document | 7t8m_full_validation.pdf.gz | 486.8 KB | Display | |
Data in XML | 7t8m_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 7t8m_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/7t8m ftp://data.pdbj.org/pub/pdb/validation_reports/t8/7t8m | HTTPS FTP |
-Related structure data
Related structure data | 7mb4C 7mb5C 7mb6C 7mb7C 7mb8C 7mb9C 7t70C 7t8rC 7t9yC 7ta4C 7ta7C 7tb2C 7tbtC 7tc4C 7l0dS 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
#1: Protein | Mass: 33793.480 Da / Num. of mol.: 2 / Mutation: C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Protein/peptide | Mass: 1094.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia (bacteria) #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 10-20 % (w/v) PEG 3350, 0.20-0.30 M NaCl, and 0.1 M Bis-Tris methane pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→24.14 Å / Num. obs: 85584 / % possible obs: 92.38 % / Redundancy: 5.5 % / Biso Wilson estimate: 10.18 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05001 / Rpim(I) all: 0.02245 / Rrim(I) all: 0.05518 / Net I/σ(I): 22.08 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4511 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 7267 / CC1/2: 0.813 / CC star: 0.947 / Rpim(I) all: 0.2971 / Rrim(I) all: 0.5427 / % possible all: 79.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7L0D Resolution: 1.6→24.14 Å / SU ML: 0.157 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.1243 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: 15.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→24.14 Å
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Refine LS restraints |
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LS refinement shell |
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