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- PDB-8dj4: NMR Solution Structure of C-terminally amidated, Full-length Huma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dj4 | ||||||
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Title | NMR Solution Structure of C-terminally amidated, Full-length Human Galanin | ||||||
![]() | Galanin | ||||||
![]() | NEUROPEPTIDE / synthetic | ||||||
Function / homology | ![]() galanin receptor binding / type 1 galanin receptor binding / type 2 galanin receptor binding / type 3 galanin receptor binding / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / positive regulation of timing of catagen / positive regulation of cortisol secretion / regulation of glucocorticoid metabolic process / negative regulation of lymphocyte proliferation ...galanin receptor binding / type 1 galanin receptor binding / type 2 galanin receptor binding / type 3 galanin receptor binding / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / positive regulation of timing of catagen / positive regulation of cortisol secretion / regulation of glucocorticoid metabolic process / negative regulation of lymphocyte proliferation / neuropeptide hormone activity / feeding behavior / insulin secretion / response to immobilization stress / neuropeptide signaling pathway / protein kinase A signaling / Peptide ligand-binding receptors / cAMP-mediated signaling / secretory granule / response to insulin / response to estrogen / G alpha (i) signalling events / response to xenobiotic stimulus / positive regulation of apoptotic process / neuronal cell body / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Wilkinson, R.E. / Kraichely, K.N. / Buchanan, L.E. / Parnham, S. / Giuliano, M.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The neuropeptide galanin adopts an irregular secondary structure. Authors: Wilkinson, R.E. / Kraichely, K.N. / Hendy, C.M. / Buchanan, L.E. / Parnham, S. / Giuliano, M.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.2 KB | Display | ![]() |
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PDB format | ![]() | 209.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 352.1 KB | Display | ![]() |
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Full document | ![]() | 467.2 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dhzC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 3159.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The authors state the following regarding the geometric deviations with this ensemble: With most of the hydrogen bonds in the N-terminus of the peptide bifurcated, or even more, they are ...Text: The authors state the following regarding the geometric deviations with this ensemble: With most of the hydrogen bonds in the N-terminus of the peptide bifurcated, or even more, they are confident that the ensemble represents the time-averaged structure of a peptide that is rapidly interconverting turns of alpha, 310-, and pi-helix. Their shift assignments were largely unambiguous and can be found in BMRB entry 31032. The "irregular helix restraints" used (and described in the manuscript and its references) were employed to allow the ensemble to sample multiple arrangements during simulated annealing. By definition, this ensemble existing as an average will display a significant degree of geometric irregularity, particularly with regard the backbone and sidechain outliers as compared to statistical norms. Further, the clashscore level is quite high. This appears to be a consequence of the very high density of ROE-derived distance restraints in the N-terminus of the peptide, which were maximally relaxed to account for any uncertainty in their measurement throughout several rounds of validation and re-calculation. Tight sidechain packing and compression seems to be the dictated outcome of our data. Much of their study is concerned with compact hydrophobic packing in this sequence - this full-length peptide is indeed much more rigid across the stretch of residues it shares with fragment peptides described in entries 7S3O, 7S3Q, and 7S3R. Together with the compactness of the region of the sequence, the clashes appear to be a consequence of several averaged, coiling, helical conformers all existing on the NMR timescale. This is discussed at further length in the citation affiliated with this deposition |
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Sample preparation
Details | Type: lyophilized powder Contents: 0.5 mM hGal(1-30)NH2, 4.14 mM [U-2H] sodium acetate, 5.86 mM [U-2H] acetic acid, 95% H2O/5% D2O Details: peptide was suspended and dissolved into deuterated acetate buffer, which had been prepared in 95:5 H2O:D2O to within 0.02 units of pH 4.6 Label: 1 / Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: sample was dissolved in 10 mM sodium acetate-d3/acetic acid-d4 buffer at pH 4.6; no additional additives were present. mM Label: 1 / pH: 4.6 / PH err: 0.02 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TCI H-C/N-D Cryoprobe |
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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: 1000 / Conformers submitted total number: 25 |