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- PDB-7tx3: Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tx3 | |||||||||
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Title | Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P43 crystal form) | |||||||||
![]() | Non-structural protein 3 | |||||||||
![]() | VIRAL PROTEIN / SARS-CoV-2 / room temperature diffraction / protein dynamics / water networks | |||||||||
Function / homology | ![]() 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 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 / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Correy, G.J. / Fraser, J.S. / Meilleur, F. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.7 KB | Display | ![]() |
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PDB format | ![]() | 132.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.6 KB | Display | ![]() |
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Full document | ![]() | 398.8 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7twfC ![]() 7twgC ![]() 7twhC ![]() 7twiC ![]() 7twjC ![]() 7twnC ![]() 7twoC ![]() 7twpC ![]() 7twqC ![]() 7twrC ![]() 7twsC ![]() 7tx4C ![]() 7tx5C ![]() 7kqoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18178.766 Da / Num. of mol.: 2 / Fragment: macrodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-NHE / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 100 mM CHES pH 9.5, 34% PEG 3000 |
-Data collection
Diffraction |
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Radiation |
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Reflection | Entry-ID: 7TX3
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Reflection shell |
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Processing
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Refinement | Biso max: 65.62 Å2 / Biso mean: 22.64 Å2 / Biso min: 11.06 Å2 / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / Method to determine structure:
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Refinement step | Cycle: LAST / Resolution: 1.6→23.14 Å
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Refine LS restraints |
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LS refinement shell |
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