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Yorodumi- PDB-7orw: Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7orw | |||||||||
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Title | Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00265 | |||||||||
Components | Non-structural protein 10 | |||||||||
Keywords | VIRAL PROTEIN / Fragment / complex / small molecule | |||||||||
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: 1.95 Å | |||||||||
Authors | Talibov, V.O. / Kozielski, F. / Sele, C. / Lou, J. / Dong, D. / Wang, Q. / Shi, X. / Nyblom, M. / Rogstam, A. / Krojer, T. ...Talibov, V.O. / Kozielski, F. / Sele, C. / Lou, J. / Dong, D. / Wang, Q. / Shi, X. / Nyblom, M. / Rogstam, A. / Krojer, T. / Knecht, W. / Fisher, S.Z. | |||||||||
Funding support | Sweden, United Kingdom, 2items
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Citation | Journal: Rsc Chem Biol / Year: 2022 Title: Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16. Authors: Kozielski, F. / Sele, C. / Talibov, V.O. / Lou, J. / Dong, D. / Wang, Q. / Shi, X. / Nyblom, M. / Rogstam, A. / Krojer, T. / Fisher, Z. / Knecht, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7orw.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7orw.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 7orw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7orw_validation.pdf.gz | 752.5 KB | Display | wwPDB validaton report |
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Full document | 7orw_full_validation.pdf.gz | 752.5 KB | Display | |
Data in XML | 7orw_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 7orw_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/7orw ftp://data.pdbj.org/pub/pdb/validation_reports/or/7orw | HTTPS FTP |
-Related structure data
Related structure data | 7orrC 7oruC 7orvC 6zpeS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13284.236 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 |
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-Non-polymers , 6 types, 93 molecules
#2: Chemical | #3: Chemical | ChemComp-7WA / | #4: Chemical | ChemComp-GOL / | #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: 3.93 Å3/Da / Density % sol: 68.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: Protein - 63 mg/mL in 50 mM Tris/HCl pH 8.0, 150 mM NaCl; precipitant (reservoir) - 0.1 M Bis-Tris/HCl pH 6.7, 2.4 M NaCl; 1:1, 1:2, 2:1 protein-to-precipitant ratios, 300 nL total drop ...Details: Protein - 63 mg/mL in 50 mM Tris/HCl pH 8.0, 150 mM NaCl; precipitant (reservoir) - 0.1 M Bis-Tris/HCl pH 6.7, 2.4 M NaCl; 1:1, 1:2, 2:1 protein-to-precipitant ratios, 300 nL total drop volume. Soaking: reservoir solution, supplemented to 50 mM ligand, 5% (v/v) DMSO, 15% (v/v) glycerol; 2 h, 293K. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9788 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→76.21 Å / Num. obs: 15364 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.028 / Rrim(I) all: 0.08 / Net I/σ(I): 13.5 / Num. measured all: 129317 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZPE Resolution: 1.95→53.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.939 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.1 Å2 / Biso mean: 48.539 Å2 / Biso min: 37.06 Å2
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Refinement step | Cycle: final / Resolution: 1.95→53.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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