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Yorodumi- PDB-2nb8: Solution structure of C-terminal extramembrane domain of SH protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nb8 | ||||||
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Title | Solution structure of C-terminal extramembrane domain of SH protein | ||||||
Components | Small hydrophobic protein | ||||||
Keywords | VIRAL PROTEIN / Bicelles / Small Hydrophobic Protein / viroporin | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis => GO:0052151 / : / symbiont-mediated suppression of host apoptosis / Translation of respiratory syncytial virus mRNAs / : / : / RSV-host interactions / Maturation of hRSV A proteins / host cell Golgi membrane / Assembly and release of respiratory syncytial virus (RSV) virions ...symbiont-mediated activation of host apoptosis => GO:0052151 / : / symbiont-mediated suppression of host apoptosis / Translation of respiratory syncytial virus mRNAs / : / : / RSV-host interactions / Maturation of hRSV A proteins / host cell Golgi membrane / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / monoatomic cation channel activity / protein complex oligomerization / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus A2 | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Li, Y. / To, J. / Surya, W. / Torres, J. | ||||||
Citation | Journal: J.Virol. / Year: 2014 Title: Inhibition of the human respiratory syncytial virus small hydrophobic protein and structural variations in a bicelle environment. Authors: Li, Y. / To, J. / Verdia-Baguena, C. / Dossena, S. / Surya, W. / Huang, M. / Paulmichl, M. / Liu, D.X. / Aguilella, V.M. / Torres, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nb8.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nb8.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 2nb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nb8_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 2nb8_full_validation.pdf.gz | 550.3 KB | Display | |
Data in XML | 2nb8_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2nb8_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/2nb8 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/2nb8 | 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: 3209.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A2 / Strain: A2 / Gene: 1A, SH / Production host: Escherichia coli (E. coli) / References: UniProt: P04852, UniProt: P0DOE5*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 | Contents: 10 % [U-2H] D2O-1, 0.7 mM [U-13C; U-15N] entity-2, 9.5 % DHPC-DLPC-3, 20 mM sodium phosphate-4, 50 mM sodium chloride-5, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 70 / pH: 5.5 / Pressure: ambient / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |