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Yorodumi- PDB-2hsx: NMR Structure of the nonstructural protein 1 (nsp1) from the SARS... -
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-Basic information
Entry | Database: PDB / ID: 2hsx | ||||||
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Title | NMR Structure of the nonstructural protein 1 (nsp1) from the SARS coronavirus | ||||||
Components | Leader protein; p65 homolog; NSP1 (EC 3.4.22.-) | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE / LEADER PROTEIN / BETA-BARREL / ALPHA-BETA / VIRUS / REPLICASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG | ||||||
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 ...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 / viral transcription / SARS-CoV-1 modulates host translation machinery / 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 / symbiont-mediated suppression of host gene expression / 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 / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 / protein dimerization activity / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | SOLUTION NMR / ATNOS, CANDID, CYANA | ||||||
Authors | Almeida, M.S. / Herrmann, T. / Geralt, M. / Johnson, M.A. / Saikatendu, K. / Joseph, J. / Subramanian, R.C. / Neuman, B.W. / Buchmeier, M.J. / Stevens, R.C. ...Almeida, M.S. / Herrmann, T. / Geralt, M. / Johnson, M.A. / Saikatendu, K. / Joseph, J. / Subramanian, R.C. / Neuman, B.W. / Buchmeier, M.J. / Stevens, R.C. / Kuhn, P. / Wilson, I.A. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Virol. / Year: 2007 Title: Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. Authors: Almeida, M.S. / Johnson, M.A. / Herrmann, T. / Geralt, M. / Wuthrich, K. #1: Journal: J.Biomol.NMR / Year: 2006 Title: NMR assignment of the SARS-CoV protein nsp1 Authors: Almeida, M.S. / Johnson, M.A. / Wuthrich, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hsx.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hsx.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hsx_validation.pdf.gz | 245.8 KB | Display | wwPDB validaton report |
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Full document | 2hsx_full_validation.pdf.gz | 245.6 KB | Display | |
Data in XML | 2hsx_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 2hsx_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/2hsx ftp://data.pdbj.org/pub/pdb/validation_reports/hs/2hsx | HTTPS FTP |
-Related structure data
Related structure data | 2gdtC 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: 12680.526 Da / Num. of mol.: 1 / Fragment: NSP1-6 / Mutation: T1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Plasmid: PSTEF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2 mM NSP1-6; 25 mM NaPHOSPHATE PH 7.0, 250 mM NACL, 10% D2O Solvent system: 25 mM NaPHOSPHATE PH 7.0, 250 mM NACL, 10% D2O |
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Sample conditions | Ionic strength: 25 mM SODIUM PHOSPHATE AND 250 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: ATNOS, CANDID, CYANA / Software ordinal: 1 / Details: v.1.0 | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Closest to the mean structure / Conformers calculated total number: 120 / Conformers submitted total number: 1 |