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Yorodumi- PDB-2k87: NMR STRUCTURE OF A PUTATIVE RNA BINDING PROTEIN (SARS1) FROM SARS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k87 | ||||||
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Title | NMR STRUCTURE OF A PUTATIVE RNA BINDING PROTEIN (SARS1) FROM SARS CORONAVIRUS | ||||||
Components | Non-structural protein 3 of Replicase polyprotein 1a | ||||||
Keywords | viral protein / RNA binding protein / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / 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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / 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 / 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 / methylation / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | NMR structure of the SARS Coronavirus nsp3e domain Nucleic Acid Binding NAB | ||||||
Model type details | minimized average | ||||||
Authors | Serrano, P. / Wuthrich, K. / Johnson, M.A. / Chatterjee, A. / Wilson, I. / Pedrini, B.F. / Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Virol. / Year: 2009 Title: Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3. Authors: Serrano, P. / Johnson, M.A. / Chatterjee, A. / Neuman, B.W. / Joseph, J.S. / 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 | 2k87.cif.gz | 717.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k87.ent.gz | 600.8 KB | Display | PDB format |
PDBx/mmJSON format | 2k87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k87_validation.pdf.gz | 474.2 KB | Display | wwPDB validaton report |
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Full document | 2k87_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2k87_validation.xml.gz | 189 KB | Display | |
Data in CIF | 2k87_validation.cif.gz | 136.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/2k87 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/2k87 | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 13230.087 Da / Num. of mol.: 1 Fragment: NAB domain of the SARS coronavirus nsp3, residues 1884-1999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Species: coronavirus / Gene: 1a / Plasmid: pET25b / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P0C6U8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: NMR structure of the SARS Coronavirus nsp3e domain Nucleic Acid Binding NAB | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.4 mM [U-99% 13C; U-99% 15N] SARS-CoV nsp3e, 2 mM sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 0.1 mM DSS, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.2 / 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: minimized average structure | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 80 / Conformers submitted total number: 20 |