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Yorodumi- PDB-7kr1: Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kr1 | ||||||
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Title | Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 310 K) | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | VIRAL PROTEIN / Macrodomain / ADP-ribose / SARS-CoV-2 | ||||||
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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent 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 | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Correy, G.J. / Young, I.D. / Thompson, M.C. / Fraser, J.S. | ||||||
Funding support | 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Authors: Schuller, M. / Correy, G.J. / Gahbauer, S. / Fearon, D. / Wu, T. / Diaz, R.E. / Young, I.D. / Carvalho Martins, L. / Smith, D.H. / Schulze-Gahmen, U. / Owens, T.W. / Deshpande, I. / Merz, G. ...Authors: Schuller, M. / Correy, G.J. / Gahbauer, S. / Fearon, D. / Wu, T. / Diaz, R.E. / Young, I.D. / Carvalho Martins, L. / Smith, D.H. / Schulze-Gahmen, U. / Owens, T.W. / Deshpande, I. / Merz, G.E. / Thwin, A.C. / Biel, J.T. / Peters, J.K. / Moritz, M. / Herrera, N. / Kratochvil, H.T. / Aimon, A. / Bennett, J.M. / Brandao Neto, J. / Cohen, A.E. / Dias, A. / Douangamath, A. / Dunnett, L. / Fedorov, O. / Ferla, M.P. / Fuchs, M.R. / Gorrie-Stone, T.J. / Holton, J.M. / Johnson, M.G. / Krojer, T. / Meigs, G. / Powell, A.J. / Rack, J.G.M. / Rangel, V.L. / Russi, S. / Skyner, R.E. / Smith, C.A. / Soares, A.S. / Wierman, J.L. / Zhu, K. / O'Brien, P. / Jura, N. / Ashworth, A. / Irwin, J.J. / Thompson, M.C. / Gestwicki, J.E. / von Delft, F. / Shoichet, B.K. / Fraser, J.S. / Ahel, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kr1.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kr1.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 7kr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kr1_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 7kr1_full_validation.pdf.gz | 419.3 KB | Display | |
Data in XML | 7kr1_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7kr1_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/7kr1 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/7kr1 | HTTPS FTP |
-Related 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
#1: Protein | Mass: 18548.027 Da / Num. of mol.: 1 / Fragment: macrodomain (UNP residues 1024-1192) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris, pH 8.5, 100 mM sodium acetate, 28% PEG4000 |
-Data collection
Diffraction | Mean temperature: 310 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03314 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03314 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→66.6 Å / Num. obs: 22439 / % possible obs: 99.99 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1932 / Rpim(I) all: 0.04451 / Net I/σ(I): 9.07 |
Reflection shell | Resolution: 1.55→1.605 Å / Redundancy: 19.9 % / Rmerge(I) obs: 3.87 / Mean I/σ(I) obs: 0.51 / Num. unique obs: 2242 / CC1/2: 0.399 / Rpim(I) all: 0.8803 / % possible all: 99.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7KR0 Resolution: 1.55→66.6 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
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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 max: 92.14 Å2 / Biso mean: 30.2616 Å2 / Biso min: 14.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→66.6 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %
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