+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2c2l | ||||||
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タイトル | Crystal structure of the CHIP U-box E3 ubiquitin ligase | ||||||
要素 |
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キーワード | CHAPERONE (シャペロン) / E3 LIGASE (ユビキチンリガーゼ) / UBIQUITINYLATION (ユビキチン) / TPR / HEAT-SHOCK PROTEIN COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 : / positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / ubiquitin conjugating enzyme complex ...: / positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / Antigen processing: Ubiquitination & Proteasome degradation / misfolded protein binding / protein folding chaperone complex / cellular response to misfolded protein / positive regulation of ubiquitin-protein transferase activity / ubiquitin-ubiquitin ligase 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 / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / protein quality control for misfolded or incompletely synthesized proteins / 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 / SMAD binding / protein monoubiquitination / protein K63-linked ubiquitination / regulation of postsynaptic membrane neurotransmitter receptor levels / negative regulation of smooth muscle cell apoptotic process / dendritic growth cone / positive regulation of proteolysis / R-SMAD binding / protein maturation / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / skeletal muscle contraction / protein unfolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / protein autoubiquitination / RHOBTB2 GTPase cycle / ubiquitin ligase complex / DNA polymerase binding / positive regulation of lamellipodium assembly / axonal growth cone / eNOS activation / : / endoplasmic reticulum unfolded protein response / endocytic vesicle lumen / 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 / positive regulation of defense response to virus by host / Signaling by ERBB2 / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / response to salt stress / positive regulation of telomerase activity / Hsp70 protein binding / Recruitment of NuMA to mitotic centrosomes / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / positive regulation of interferon-beta production / activation of innate immune response / response to cold 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: 3.3 Å | ||||||
データ登録者 | Zhang, M. / Roe, S.M. / Pearl, L.H. | ||||||
引用 | ジャーナル: Mol.Cell / 年: 2005 タイトル: Chaperoned Ubiquitylation-Crystal Structures of the Chip U Box E3 Ubiquitin Ligase and a Chip-Ubc13-Uev1A Complex 著者: Zhang, M. / Windheim, M. / Roe, S.M. / Peggie, M. / Cohen, P. / Prodromou, C. / Pearl, L.H. | ||||||
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 | 2c2l.cif.gz | 235.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2c2l.ent.gz | 198.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2c2l.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/c2/2c2l ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c2l | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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-要素
#1: タンパク質 | 分子量: 32728.904 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: Q9DCJ0, UniProt: Q9WUD1*PLUS #2: タンパク質・ペプチド | 分子量: 1082.120 Da / 分子数: 4 / Fragment: C-TERMINAL PEPTIDE, UNP RESIDUES 414-422 / 由来タイプ: 合成 / 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: Q96HX7, UniProt: P07900*PLUS #3: 化合物 | ChemComp-SO4 / #4: 化合物 | ChemComp-NI / #5: 水 | ChemComp-HOH / | |
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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: 4.4 Å3/Da / 溶媒含有率: 71.5 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法 / pH: 7.5 詳細: MCHIP WAS MIXED WITH HUMAN HSP90 C-TERMINAL PEPTIDE AT A 1:3 MOLAR RATIO, RESPECTIVELY, INCUBATED FOR 30 MIN AT 4C AND CONCENTRATED TO 10 MG/ML. INITIAL MULTIPLE CRYSTALS WERE GROWN BY VAPOUR ...詳細: MCHIP WAS MIXED WITH HUMAN HSP90 C-TERMINAL PEPTIDE AT A 1:3 MOLAR RATIO, RESPECTIVELY, INCUBATED FOR 30 MIN AT 4C AND CONCENTRATED TO 10 MG/ML. INITIAL MULTIPLE CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20C AGAINST 30% W/V PEG4000, 100 MM TRIS [PH 7.5] AND 200 MM LITHIUM SULPHATE. SUBSEQUENT STREAK-SEEDING INTO SOLUTIONS OF 16% W/V PEG4000, 100 MM TRIS [PH 7.5] AND 400 MM LITHIUM SULPHATE PRODUCED SINGLE PLATES. |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID23-1 / 波長: 0.9801 |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2005年3月17日 |
放射 | 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: 0.9801 Å / 相対比: 1 |
反射 | 解像度: 3.3→40 Å / Num. obs: 68272 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / 冗長度: 2.1 % / Biso Wilson estimate: 84.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10 |
反射 シェル | 解像度: 3.3→3.47 Å / 冗長度: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / % possible all: 98.1 |
-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: IN-HOUSE MODEL 解像度: 3.3→40 Å / Data cutoff high absF: 10000 / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
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溶媒の処理 | 溶媒モデル: FLAT / Bsol: 14.9172 Å2 / ksol: 0.307367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 80.1 Å2
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精密化ステップ | サイクル: LAST / 解像度: 3.3→40 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3.3→3.49 Å / Total num. of bins used: 7
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Xplor file |
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