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Yorodumi- PDB-6xb2: Room temperature X-ray crystallography reveals catalytic cysteine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xb2 | ||||||
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Title | Room temperature X-ray crystallography reveals catalytic cysteine in the SARS-CoV-2 3CL Mpro is highly reactive: Insights for enzyme mechanism and drug design | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE / Main Protease SARS-CoV-2 3CL Mpro | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kneller, D.W. / Kovalevsky, A. / Coates, L. | ||||||
Citation | Journal: Iucrj / Year: 2020 Title: Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro : insights into enzyme mechanism and drug design. Authors: Kneller, D.W. / Phillips, G. / O'Neill, H.M. / Tan, K. / Joachimiak, A. / Coates, L. / Kovalevsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xb2.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xb2.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 6xb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xb2_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 6xb2_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 6xb2_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 6xb2_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/6xb2 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xb2 | HTTPS FTP |
-Related structure data
Related structure data | 6xb0C 6xb1C 6xhuC 6wqfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DMS / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: BIS-TRIS pH=6.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.29 Å / Num. obs: 16266 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.35 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.036 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1332 / CC1/2: 0.46 / Rpim(I) all: 0.658 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WQF Resolution: 2.1→18.86 Å / SU ML: 0.279 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3122 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: 46.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→18.86 Å
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Refine LS restraints |
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LS refinement shell |
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