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Yorodumi- PDB-2ajj: NMR structure of the in-plane membrane anchor domain [1-28] of th... -
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-Basic information
Entry | Database: PDB / ID: 2ajj | ||||||
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Title | NMR structure of the in-plane membrane anchor domain [1-28] of the monotopic Non Structural Protein 5A (NS5A) of Bovine Viral Diarrhea Virus (BVDV) | ||||||
Components | Nonstructural protein 5A | ||||||
Keywords | MEMBRANE PROTEIN / in-plane membrane anchor domain / amphipathic alpha-helix | ||||||
Function / homology | Function and homology information pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell ...pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / viral protein processing / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, energy minimization | ||||||
Authors | Sapay, N. / Montserret, R. / Chipot, C. / Brass, V. / Moradpour, D. / Deleage, G. / Penin, F. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: NMR structure and molecular dynamics of the in-plane membrane anchor of nonstructural protein 5A from bovine viral diarrhea virus. Authors: Sapay, N. / Montserret, R. / Chipot, C. / Brass, V. / Moradpour, D. / Deleage, G. / Penin, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ajj.cif.gz | 283.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ajj.ent.gz | 235.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ajj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/2ajj ftp://data.pdbj.org/pub/pdb/validation_reports/aj/2ajj | HTTPS FTP |
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-Related structure data
Related structure data | 2ajmC 2ajnC 2ajoC 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/peptide | Mass: 3204.788 Da / Num. of mol.: 1 / Fragment: BVDV NS5A / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence is naturally found in Bovine viral diarrhea virus 1, strain CP7. References: UniProt: Q96662 |
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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 BVDV NS5A[1-28], 50% 2,2,2-TriFluoroEthanol-d2 , 50% H2O Solvent system: 50% TFE-d2, 50% H2O | |||||||||||||||
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, energy minimization Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 31 |