[English] 日本語
Yorodumi- PDB-2kaf: Solution structure of the SARS-unique domain-C from the nonstruct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kaf | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the SARS-unique domain-C from the nonstructural protein 3 (nsp3) of the severe acute respiratory syndrome coronavirus | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | viral protein / RNA binding protein / SARS coronavirus / nonstructural protein 3 / SARS-unique domain-C / automation in NMR structure determination / hydrolase. Joint Center for Structural Genomics. JCSG. PSI / Protein Structure Initiative | ||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / methylation / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / viral protein processing / lyase activity / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | SOLUTION NMR / torsion angle dynamics, energy minimization | ||||||
Authors | Johnson, M.A. / Mohanty, B. / Pedrini, B. / Serrano, P. / Chatterjee, A. / Herrmann, T. / Joseph, J. / Saikatendu, K. / Wilson, I.A. / Buchmeier, M.J. ...Johnson, M.A. / Mohanty, B. / Pedrini, B. / Serrano, P. / Chatterjee, A. / Herrmann, T. / Joseph, J. / Saikatendu, K. / Wilson, I.A. / Buchmeier, M.J. / Kuhn, P. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding. Authors: Johnson, M.A. / Chatterjee, A. / Neuman, B.W. / Wuthrich, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2kaf.cif.gz | 404.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2kaf.ent.gz | 352.9 KB | Display | PDB format |
PDBx/mmJSON format | 2kaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/2kaf ftp://data.pdbj.org/pub/pdb/validation_reports/ka/2kaf | HTTPS FTP |
---|
-Related structure data
Related structure data | 2kqvC 2kqwC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 7596.431 Da / Num. of mol.: 1 / Fragment: SARS-unique domain-C, residues 1473-1532 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Gene: 1a / Plasmid: pET-28b / Species (production host): coli / Production host: Escherichia coli (E. coli) References: UniProt: P0C6U8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 20 mM sodium chloride, 2.8 mM sodium azide, 20 mM sodium phosphate, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
Sample conditions | Ionic strength: 0.0628 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics, energy minimization / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20 |