+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8agi | ||||||
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タイトル | Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) in complex with JMC31 | ||||||
要素 | Heat shock protein HSP 90-alphaHeat shock response | ||||||
キーワード | CHAPERONE (シャペロン) / Hsp90 (Hsp90) / NTD / 1 / 2 / 3-triazole-based compound / complex | ||||||
機能・相同性 | 機能・相同性情報 sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity ...sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / positive regulation of cell size / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / axonal growth cone / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / positive regulation of telomerase activity / Signaling by ERBB2 / positive regulation of defense response to virus by host / endocytic vesicle lumen / response to salt stress / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / nitric-oxide synthase regulator activity / response to cold / positive regulation of interferon-beta production / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition / disordered domain specific binding / unfolded protein binding / メラノソーム 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 Å | ||||||
データ登録者 | Tassone, G. / Pozzi, C. / Mazzorana, M. / Mangani, S. / Maramai, S. | ||||||
資金援助 | 1件
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引用 | ジャーナル: Int J Mol Sci / 年: 2022 タイトル: Structural Characterization of Human Heat Shock Protein 90 N-Terminal Domain and Its Variants K112R and K112A in Complex with a Potent 1,2,3-Triazole-Based Inhibitor. 著者: Tassone, G. / Mazzorana, M. / Mangani, S. / Petricci, E. / Cini, E. / Giannini, G. / Pozzi, C. / Maramai, S. | ||||||
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 | 8agi.cif.gz | 100.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8agi.ent.gz | 74.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8agi.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/ag/8agi ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agi | HTTPS FTP |
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-関連構造データ
関連構造データ | 8agjC 8aglC 6gq6S S: 精密化の開始モデル 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 |
-リンク
-集合体
登録構造単位 |
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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 28773.145 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HSP90AA1, HSP90A, HSPC1, HSPCA / プラスミド: pET28b / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P07900 #2: 化合物 | #3: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.45 Å3/Da / 溶媒含有率: 49.77 % |
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結晶化 | 温度: 281 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: 25% wt/vol PEG-4000, 200 mM magnesium chloride and 100 mM TRIS-HCl, pH 8.5 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.9795 Å |
検出器 | タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2022年5月13日 |
放射 | モノクロメーター: Si(111) / 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: 0.9795 Å / 相対比: 1 |
反射 | 解像度: 2.1→212.19 Å / Num. obs: 30642 / % possible obs: 88.6 % / 冗長度: 13 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Rrim(I) all: 0.057 / Net I/σ(I): 24.5 |
反射 シェル | 解像度: 2.1→2.21 Å / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4410 / CC1/2: 0.871 / Rpim(I) all: 0.225 / Rrim(I) all: 0.788 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 6GQ6 解像度: 2.1→68.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.941 / SU ML: 0.153 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.211 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: U VALUES : REFINED INDIVIDUALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 111.57 Å2 / Biso mean: 45.436 Å2 / Biso min: 21.36 Å2
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精密化ステップ | サイクル: final / 解像度: 2.1→68.94 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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