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Yorodumi- PDB-2bbp: NMR structures of the peptide linked to the genome (VPg) of poliovirus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bbp | ||||||
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Title | NMR structures of the peptide linked to the genome (VPg) of poliovirus | ||||||
Components | Genome linked protein VPg | ||||||
Keywords | VIRAL PROTEIN / VPg / RNA transcription primer / flexible structure / viral polymerase / picornavirus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / 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 / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Method | SOLUTION NMR / automatic NOE assignment in combination with distance geometry | ||||||
Authors | Schein, C.H. / Oezguen, N. | ||||||
Citation | Journal: Peptides / Year: 2006 Title: NMR structure of the viral peptide linked to the genome (VPg) of poliovirus. Authors: Schein, C.H. / Oezguen, N. / Volk, D.E. / Garimella, R. / Paul, A. / Braun, W. #1: Journal: Proteins / Year: 2006 Title: Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses Authors: Schein, C.H. / Volk, D.E. / Oezguen, N. / Paul, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bbp.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bbp.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bbp_validation.pdf.gz | 339.5 KB | Display | wwPDB validaton report |
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Full document | 2bbp_full_validation.pdf.gz | 400.9 KB | Display | |
Data in XML | 2bbp_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 2bbp_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/2bbp ftp://data.pdbj.org/pub/pdb/validation_reports/bb/2bbp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2357.749 Da / Num. of mol.: 1 / Fragment: residues 1-22 / Source method: obtained synthetically Details: This sequence occurs naturally in human poliovirus serotype 1. References: UniProt: P03300 |
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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: 3.7 mM peptide, 10 mM Na phosphate buffer, pH 7.2, DSS, 10% D20, 90% H2O Solvent system: 10% D20, 90% H2O |
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Sample conditions | Ionic strength: 10 mM / pH: 7.2 / Pressure: 1 atm / Temperature: 283 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: automatic NOE assignment in combination with distance geometry Software ordinal: 1 Details: Refinement of the NOE assignment is performed iteratively. NOAH passes geometrical constraints derived from the NOE list to DIAMOD. DIAMOD calculates a bundle of structures with least ...Details: Refinement of the NOE assignment is performed iteratively. NOAH passes geometrical constraints derived from the NOE list to DIAMOD. DIAMOD calculates a bundle of structures with least violation of the constraints. The new bundle of structures is the basis for refinement of the assignments in NOAH. | ||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 10 |