[English] 日本語
Yorodumi- PDB-7rls: Room temperature X-ray structure of SARS-CoV-2 main protease (Mpr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rls | ||||||
---|---|---|---|---|---|---|---|
Title | Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-68 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE/INHIBITOR / cysteine protease / inhibitor complex / HYDROLASE / 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 / 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 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kovalevsky, A. / Kneller, D.W. / Coates, L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. Authors: Kneller, D.W. / Li, H. / Galanie, S. / Phillips, G. / Labbe, A. / Weiss, K.L. / Zhang, Q. / Arnould, M.A. / Clyde, A. / Ma, H. / Ramanathan, A. / Jonsson, C.B. / Head, M.S. / Coates, L. / ...Authors: Kneller, D.W. / Li, H. / Galanie, S. / Phillips, G. / Labbe, A. / Weiss, K.L. / Zhang, Q. / Arnould, M.A. / Clyde, A. / Ma, H. / Ramanathan, A. / Jonsson, C.B. / Head, M.S. / Coates, L. / Louis, J.M. / Bonnesen, P.V. / Kovalevsky, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rls.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rls.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rls_validation.pdf.gz | 723.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7rls_full_validation.pdf.gz | 725.5 KB | Display | |
Data in XML | 7rls_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7rls_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/7rls ftp://data.pdbj.org/pub/pdb/validation_reports/rl/7rls | HTTPS FTP |
-Related structure data
Related structure data | 7n8cC 7rm2C 7rmbC 7rmeC 7rmtC 7rmzC 7rn4C 7rnhC 7rnkC 7ltjS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 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 |
---|---|
#2: Chemical | ChemComp-5YN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.33 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 18-21% PEG3350, 0.1 M Bis-Tris pH 6.5 or pH 7.0 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2→60.96 Å / Num. obs: 25988 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.041 / Net I/σ(I): 14.26 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 2594 / CC1/2: 0.722 / Rpim(I) all: 0.281 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LTJ Resolution: 2→27.34 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→27.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|