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Yorodumi- PDB-2rnk: NMR structure of the domain 513-651 of the SARS-CoV nonstructural... -
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-Basic information
Entry | Database: PDB / ID: 2rnk | |||||||||
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Title | NMR structure of the domain 513-651 of the SARS-CoV nonstructural protein nsp3 | |||||||||
Components | Replicase polyprotein 1ab | |||||||||
Keywords | VIRAL PROTEIN / SARS-CoV / SARS-unique domain / nonstructural protein / nsp3 / nsp3c / Functional and Structural Proteomics of SARS-CoV-Related Proteins / FSPS / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / ATP-binding / Cytoplasm / Endonuclease / Exonuclease / Helicase / Hydrolase / Membrane / Metal-binding / Nuclease / Nucleotide-binding / Nucleotidyltransferase / Protease / Ribosomal frameshift / RNA replication / RNA-binding / RNA-directed RNA polymerase / Thiol protease / Transferase / Transmembrane / Zinc / Zinc-finger | |||||||||
Function / homology | Function and homology information viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex ...viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex / : / mRNA capping enzyme complex / suppression by virus of host type I interferon production / positive stranded viral RNA replication / positive regulation of RNA biosynthetic process / protein K48-linked deubiquitination / : / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K63-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / viral transcription / protein autoprocessing / 7-methylguanosine mRNA capping / positive regulation of viral genome replication / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / symbiont-mediated suppression of host gene expression / 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 / 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 / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / protein dimerization activity / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | SARS coronavirus | |||||||||
Method | SOLUTION NMR / torsion angle dynamics | |||||||||
Model details | The middle domain of the SARS-unique region of the nonstructural protein 3 of the SARS coronavirus | |||||||||
Authors | Chatterjee, A. / Johnson, M.A. / Serrano, P. / Pedrini, B. / Joseph, J. / Saikatendu, K. / Neuman, B.W. / Wilson, I.A. / Stevens, R.C. / Buchmeier, M.J. ...Chatterjee, A. / Johnson, M.A. / Serrano, P. / Pedrini, B. / Joseph, J. / Saikatendu, K. / Neuman, B.W. / Wilson, I.A. / Stevens, R.C. / Buchmeier, M.J. / Kuhn, P. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: J.Virol. / Year: 2009 Title: Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. Authors: Chatterjee, A. / Johnson, M.A. / Serrano, P. / Pedrini, B. / Joseph, J.S. / Neuman, B.W. / Saikatendu, K. / Buchmeier, M.J. / Kuhn, P. / Wuthrich, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rnk.cif.gz | 865.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rnk.ent.gz | 724.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rnk_validation.pdf.gz | 358.8 KB | Display | wwPDB validaton report |
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Full document | 2rnk_full_validation.pdf.gz | 486.7 KB | Display | |
Data in XML | 2rnk_validation.xml.gz | 44.7 KB | Display | |
Data in CIF | 2rnk_validation.cif.gz | 72.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/2rnk ftp://data.pdbj.org/pub/pdb/validation_reports/rn/2rnk | HTTPS FTP |
-Related structure data
Related structure data | 2jzdC 2jzeC 2jzfC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15859.375 Da / Num. of mol.: 1 Fragment: Non-structural protein 3 (Domain 513-651): Residues 1331-1469 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Gene: rep, 1a-1b / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P59641, UniProt: P0C6X7*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.227 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |