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Yorodumi- PDB-7phz: Crystal structure of X77 bound to the main protease (3CLpro/Mpro)... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 7phz | ||||||
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| Title | Crystal structure of X77 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in spacegroup P2(1)2(1)2(1). | ||||||
Components | Replicase polyprotein 1ab | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / Mpro / 3CLpro / EXSCALATE4COV / drug discovery / Elettra / X77 | ||||||
| Function / homology | Function and homology informationprotein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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 | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Costanzi, E. / Demitri, N. / Storici, P. | ||||||
| Funding support | European Union, 1items
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Citation | Journal: J.Chem.Inf.Model. / Year: 2024Title: Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. Authors: Albani, S. / Costanzi, E. / Hoang, G.L. / Kuzikov, M. / Frings, M. / Ansari, N. / Demitri, N. / Nguyen, T.T. / Rizzi, V. / Schulz, J.B. / Bolm, C. / Zaliani, A. / Carloni, P. / Storici, P. / Rossetti, G. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7phz.cif.gz | 409.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb7phz.ent.gz | 306.1 KB | Display | PDB format |
| PDBx/mmJSON format | 7phz.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/7phz ftp://data.pdbj.org/pub/pdb/validation_reports/ph/7phz | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 8p54C ![]() 8p55C ![]() 8p56C ![]() 8p57C ![]() 8p58C ![]() 8p5aC ![]() 8p5bC ![]() 8p5cC ![]() 8p86C ![]() 8p87C ![]() 7bb2S S: Starting model for refinement C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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| Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
| #1: Protein | Mass: 33825.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rep, 1a-1b / Production host: ![]() |
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-Non-polymers , 6 types, 544 molecules 










| #2: Chemical | | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | Y |
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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: 2.63 Å3/Da / Density % sol: 53.26 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris/BICINE pH 8.5; 0.12M D-Glucose; 0.12M D-Mannose; 0.12M D-Galactose; 0.12M L-Fucose; 0.12M D-Xylose; 0.12M N-Acetyl-D-Glucosamine; 20% v/v Ethylene glycol; 10 % w/v PEG 8000 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2021 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 1.66→104.39 Å / Num. obs: 84823 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 22.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.8 |
| Reflection shell | Resolution: 1.66→1.69 Å / Num. unique obs: 4313 / CC1/2: 0.69 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 7BB2 Resolution: 1.66→41.33 Å / SU ML: 0.1589 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7463 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: 32.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.66→41.33 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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