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Yorodumi- PDB-7tx4: Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tx4 | |||||||||
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Title | Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P21 crystal form) | |||||||||
Components | Papain-like protease nsp3 | |||||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / room temperature diffraction / protein dynamics / water networks | |||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / Replication of the SARS-CoV-2 genome / 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 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Correy, G.J. / Fraser, J.S. / Kovalevsky, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Adv / Year: 2022 Title: The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Authors: Correy, G.J. / Kneller, D.W. / Phillips, G. / Pant, S. / Russi, S. / Cohen, A.E. / Meigs, G. / Holton, J.M. / Gahbauer, S. / Thompson, M.C. / Ashworth, A. / Coates, L. / Kovalevsky, A. / ...Authors: Correy, G.J. / Kneller, D.W. / Phillips, G. / Pant, S. / Russi, S. / Cohen, A.E. / Meigs, G. / Holton, J.M. / Gahbauer, S. / Thompson, M.C. / Ashworth, A. / Coates, L. / Kovalevsky, A. / Meilleur, F. / Fraser, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tx4.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tx4.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 7tx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/7tx4 ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7tx4 | HTTPS FTP |
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-Related structure data
Related structure data | 7twfC 7twgC 7twhC 7twiC 7twjC 7twnC 7twoC 7twpC 7twqC 7twrC 7twsC 7tx3C 7tx5C 7kqoS 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: 18218.721 Da / Num. of mol.: 1 / Fragment: macrodomain 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) References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES pH 6.5, 28% PEG 4000 |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 7TX4
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Reflection shell |
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-Processing
Software |
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Refinement | Biso max: 71.08 Å2 / Biso mean: 26.88 Å2 / Biso min: 10.66 Å2 / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: Flat bulk solvent model
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Refinement step | Cycle: LAST / Resolution: 1.9→25.49 Å
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Refine LS restraints |
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LS refinement shell |
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