+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4nu1 | ||||||
---|---|---|---|---|---|---|---|
タイトル | Crystal structure of a transition state mimic of the GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide | ||||||
要素 |
| ||||||
キーワード | TRANSFERASE/PEPTIDE / Wnt / LRP6 / GSK-3 (GSK-3) / Axin (AXIN1) / kinase (キナーゼ) / primed substrate / transition state (遷移状態) / phosphorylated N-terminal auto-inhibitory pS9 peptide / TRANSFERASE-PEPTIDE complex | ||||||
機能・相同性 | 機能・相同性情報 hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuron maturation / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / membrane-bounded organelle ...hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuron maturation / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / membrane-bounded organelle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of synaptic assembly at neuromuscular junction / myotube differentiation / positive regulation of osteoclast proliferation / armadillo repeat domain binding / negative regulation of neuron migration / cell growth involved in cardiac muscle cell development / positive regulation of cardiac muscle cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / head development / negative regulation of dendrite morphogenesis / Degradation of beta-catenin by the destruction complex / 細胞生物学 / neuron projection organization / regulation of microtubule anchoring at centrosome / dorsal/ventral axis specification / negative regulation of cardiac muscle hypertrophy / positive regulation of stem cell differentiation / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / protein localization to microtubule / axial mesoderm formation / negative regulation of dendrite development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of smooth muscle cell apoptotic process / GLI3 is processed to GLI3R by the proteasome / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / autosome genomic imprinting / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 減数分裂 / positive regulation of cilium assembly / bone remodeling / myoblast fusion / post-anal tail morphogenesis / negative regulation of protein acetylation / negative regulation of TOR signaling / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein serine/threonine kinase binding / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / tau-protein kinase / regulation of microtubule-based process / regulation of modification of postsynaptic structure / regulation of protein export from nucleus / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / positive regulation of osteoclast differentiation / axon extension / I-SMAD binding / negative regulation of protein metabolic process / cellular response to interleukin-3 / cellular response to glucocorticoid stimulus / Wnt signalosome / regulation of axon extension / positive regulation of mitochondrial membrane potential / regulation of long-term synaptic potentiation / 紡錘体 / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nucleocytoplasmic transport / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / regulation of osteoblast differentiation / negative regulation of fat cell differentiation / establishment or maintenance of cell polarity / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / dynein complex binding / regulation of neuronal synaptic plasticity / regulation of dendrite morphogenesis / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / response to zinc ion / glycogen metabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å | ||||||
データ登録者 | Chu, M.L.-H. / Stamos, J.L. / Enos, M.D. / Shah, N. / Weis, W.I. | ||||||
引用 | ジャーナル: Elife / 年: 2014 タイトル: Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6. 著者: Stamos, J.L. / Chu, M.L. / Enos, M.D. / Shah, N. / Weis, W.I. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 4nu1.cif.gz | 174.6 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb4nu1.ent.gz | 138.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4nu1.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/nu/4nu1 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/4nu1 | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-要素
-タンパク質 / タンパク質・ペプチド , 2種, 2分子 AB
#1: タンパク質 | 分子量: 44260.605 Da / 分子数: 1 / 断片: Residues 1-383 with phosphoylated Ser9 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Gsk3b / プラスミド: pET29b(+) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)Codon-plus RIL 参照: UniProt: Q9WV60, tau-protein kinase, non-specific serine/threonine protein kinase |
---|---|
#2: タンパク質・ペプチド | 分子量: 2738.144 Da / 分子数: 1 / 断片: Residues 383-402 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AXIN1, AXIN / プラスミド: Modified pGEX-KG / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)Codon-plus RIL / 参照: UniProt: O15169 |
-非ポリマー , 6種, 105分子
#3: 化合物 | #4: 化合物 | #5: 化合物 | ChemComp-ADP / | #6: 化合物 | ChemComp-AF3 / | #7: 化合物 | ChemComp-NO3 / | #8: 水 | ChemComp-HOH / | |
---|
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
---|
-試料調製
結晶 | マシュー密度: 2.83 Å3/Da / 溶媒含有率: 56.48 % |
---|---|
結晶化 | 温度: 277 K / 手法: microdialysis / pH: 7.5 詳細: 10% PEG 35,000, 20mM Tris pH7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K |
-データ収集
回折 | 平均測定温度: 78 K |
---|---|
放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-B / 波長: 1.033 Å |
検出器 | タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2013年11月15日 / 詳細: mirrors |
放射 | モノクロメーター: Si(III) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.033 Å / 相対比: 1 |
反射 | 解像度: 2.5→46.76 Å / Num. all: 19925 / Num. obs: 19922 / % possible obs: 100 % / Observed criterion σ(F): 0 / 冗長度: 21 % / Biso Wilson estimate: 60.85 Å2 / Rsym value: 0.303 / Net I/σ(I): 13 |
反射 シェル | 解像度: 2.5→2.6 Å / 冗長度: 21.6 % / Mean I/σ(I) obs: 0.7 / Rsym value: 6.772 / % possible all: 100 |
-位相決定
位相決定 | 手法: 分子置換 |
---|
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: 4NM3 解像度: 2.5→40.498 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.39 / σ(F): 1.35 / 位相誤差: 26.15 / 立体化学のターゲット値: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 74.7733 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.5→40.498 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 TLSグループ |
|