+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8dj4 | ||||||
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タイトル | NMR Solution Structure of C-terminally amidated, Full-length Human Galanin | ||||||
要素 | Galanin | ||||||
キーワード | NEUROPEPTIDE / synthetic | ||||||
機能・相同性 | 機能・相同性情報 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 / cAMP-mediated signaling / response to immobilization stress / neuropeptide signaling pathway / protein kinase A signaling / Peptide ligand-binding receptors / 分泌 / 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 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
データ登録者 | Wilkinson, R.E. / Kraichely, K.N. / Buchanan, L.E. / Parnham, S. / Giuliano, M.W. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Biochem.Biophys.Res.Commun. / 年: 2022 タイトル: The neuropeptide galanin adopts an irregular secondary structure. 著者: Wilkinson, R.E. / Kraichely, K.N. / Hendy, C.M. / Buchanan, L.E. / Parnham, S. / Giuliano, M.W. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8dj4.cif.gz | 246.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8dj4.ent.gz | 209.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8dj4.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/dj/8dj4 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/8dj4 | HTTPS FTP |
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-関連構造データ
関連構造データ | 8dhzC C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
その他のデータベース |
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-リンク
-集合体
登録構造単位 |
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1 |
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NMR アンサンブル |
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-要素
#1: タンパク質・ペプチド | 分子量: 3159.454 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P22466 |
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研究の焦点であるリガンドがあるか | N |
-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||||||||||||
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NMR実験 |
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NMR実験の詳細 | 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 |
-試料調製
詳細 | タイプ: lyophilized powder 内容: 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 詳細: 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 / 溶媒系: 95% H2O/5% D2O | ||||||||||||||||
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試料 |
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試料状態 | イオン強度: 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 / 圧: 1 atm / 温度: 298 K |
-NMR測定
NMRスペクトロメーター | タイプ: Bruker AVANCE III / 製造業者: Bruker / モデル: AVANCE III / 磁場強度: 600 MHz / 詳細: TCI H-C/N-D Cryoprobe |
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-解析
NMR software |
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精密化 | 手法: simulated annealing / ソフトェア番号: 1 | |||||||||||||||
代表構造 | 選択基準: lowest energy | |||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 1000 / 登録したコンフォーマーの数: 25 |