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Yorodumi- PDB-8d35: Crystal structure of SARS-CoV-2 main protease (Mpro) C145A mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d35 | ||||||
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Title | Crystal structure of SARS-CoV-2 main protease (Mpro) C145A mutant in complex with peptide from human tRNA methyltransferase TRMT1 | ||||||
Components |
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Keywords | VIRAL PROTEIN / HYDROLASE / protease / host-virus protein interaction / RNA modifying enzyme | ||||||
Function / homology | Function and homology information tRNA N2-guanine methylation / : / tRNA (guanine26-N2)-dimethyltransferase / tRNA modification in the nucleus and cytosol / tRNA modification / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases ...tRNA N2-guanine methylation / : / tRNA (guanine26-N2)-dimethyltransferase / tRNA modification in the nucleus and cytosol / tRNA modification / 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 / 5'-3' DNA helicase activity / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / tRNA binding / 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 / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / 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 / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | D'Oliviera, A. / Mugridge, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2023 Title: Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. Authors: D'Oliviera, A. / Dai, X. / Mottaghinia, S. / Geissler, E.P. / Etienne, L. / Zhang, Y. / Mugridge, J.S. #1: Journal: Biorxiv / Year: 2023 Title: Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. Authors: Da Oliviera, A. / Dai, X. / Mottaghinia, S. / Geissler, E.P. / Etienne, L. / Zhang, Y. / Mugridge, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d35.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d35.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 8d35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/8d35 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/8d35 | HTTPS FTP |
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-Related structure data
Related structure data | 7mgsS S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 33937.609 Da / Num. of mol.: 2 / Fragment: UNP residues 3264-3569 / 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 coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Protein/peptide | | Mass: 1346.534 Da / Num. of mol.: 1 / Fragment: UNP residues 526-536 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q9NXH9, tRNA (guanine26-N2)-dimethyltransferase |
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-Non-polymers , 4 types, 365 molecules
#3: Chemical | ChemComp-CL / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
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: 2.65 Å3/Da / Density % sol: 51.36 % / Description: Rhombohedral shaped plates |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 20-21.5% PEG3350, 100 mM sodium chloride, diffraction-quality crystals obtained from seeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920219 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920219 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.34 Å / Num. obs: 55694 / % possible obs: 99.08 % / Redundancy: 13.8 % / Biso Wilson estimate: 26.97 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 14 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 5409 / CC1/2: 0.656 / % possible all: 98.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7MGS Resolution: 1.9→29.34 Å / SU ML: 0.2036 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3014 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: 30.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.34 Å
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Refine LS restraints |
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LS refinement shell |
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