+Open data
-Basic information
Entry | Database: PDB / ID: 7qgi | |||||||||
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Title | Crystal structure of SARS-CoV-2 NSP14 in the absence of NSP10 | |||||||||
Components | Proofreading exoribonuclease nsp14 | |||||||||
Keywords | VIRAL PROTEIN / Nuclease / Methyltransferase / SARS-CoV-2 / NSP14 | |||||||||
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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Newman, J.A. / Imprachim, N. / Yosaatmadja, Y. / Gileadi, O. | |||||||||
Funding support | 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development. Authors: Imprachim, N. / Yosaatmadja, Y. / Newman, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qgi.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qgi.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qgi_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 7qgi_full_validation.pdf.gz | 441.5 KB | Display | |
Data in XML | 7qgi_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 7qgi_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/7qgi ftp://data.pdbj.org/pub/pdb/validation_reports/qg/7qgi | HTTPS FTP |
-Related structure data
Related structure data | 7qifC 5c8sS 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: 59534.168 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, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters | ||||||
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#2: Chemical | #3: Chemical | #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: 2.67 Å3/Da / Density % sol: 53.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.26 M sodium phosphate monobasic, 0.14 M potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→69.214 Å / Num. obs: 37654 / % possible obs: 89.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.059 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.65→1.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.075 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1884 / CC1/2: 0.716 / Rpim(I) all: 0.466 / % possible all: 65.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5c8s Resolution: 1.65→61.1 Å / SU ML: 0.1402 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.278 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: 25.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→61.1 Å
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Refine LS restraints |
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LS refinement shell |
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