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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1lm8 | ||||||
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タイトル | Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex | ||||||
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![]() | TRANSCRIPTION / REGULATION / tumor suppressor / oxygen sensing | ||||||
機能・相同性 | ![]() epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / positive regulation of mitophagy / retina vasculature development in camera-type eye / Cellular response to hypoxia / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / intracellular oxygen homeostasis / regulation of cellular response to hypoxia / negative regulation of bone mineralization / B-1 B cell homeostasis / vascular endothelial growth factor production / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / transcription regulator activator activity / dopaminergic neuron differentiation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / target-directed miRNA degradation / lactate metabolic process / elongin complex / STAT3 nuclear events downstream of ALK signaling / VCB complex / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / positive regulation of vascular endothelial growth factor receptor signaling pathway / motile cilium / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / negative regulation of TOR signaling / response to iron ion / Replication of the SARS-CoV-1 genome / response to muscle activity / Cul5-RING ubiquitin ligase complex / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / embryonic hemopoiesis / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / regulation of aerobic respiration / digestive tract morphogenesis / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / SUMOylation of ubiquitinylation proteins / positive regulation of epithelial cell migration / bone mineralization / heart looping / outflow tract morphogenesis / negative regulation of transcription elongation by RNA polymerase II / E-box binding / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / positive regulation of vascular endothelial growth factor production / TOR signaling / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / Tat-mediated elongation of the HIV-1 transcript / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / Formation of HIV-1 elongation complex containing HIV-1 Tat / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / Formation of HIV elongation complex in the absence of HIV Tat / chondrocyte differentiation / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of chemokine production / axon cytoplasm / negative regulation of TORC1 signaling / positive regulation of endothelial cell proliferation / RNA Polymerase II Pre-transcription Events / lactation / positive regulation of glycolytic process 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Min, J.-H. / Yang, H. / Ivan, M. / Gertler, F. / Kaelin JR., W.G. / Pavletich, N.P. | ||||||
![]() | ![]() タイトル: Structure of an HIF-1alpha -pVHL complex: hydroxyproline recognition in signaling. 著者: Min, J.H. / Yang, H. / Ivan, M. / Gertler, F. / Kaelin Jr., W.G. / Pavletich, N.P. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロード
PDBx/mmCIF形式 | ![]() | 98.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 74.2 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 389.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 396.4 KB | 表示 | |
XML形式データ | ![]() | 9.6 KB | 表示 | |
CIF形式データ | ![]() | 17.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1vcbS S: 精密化の開始モデル |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 13147.781 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: タンパク質 | 分子量: 10843.420 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#3: タンパク質 | 分子量: 18558.162 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#4: タンパク質・ペプチド | 分子量: 2427.726 Da / 分子数: 1 / Fragment: Residues 556-575 / 由来タイプ: 合成 詳細: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Homo sapiens. 参照: UniProt: Q16665 |
#5: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.41 Å3/Da / 溶媒含有率: 49.02 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 6.5 / 詳細: pH 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 25 ℃ / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2001年10月24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: 0.95 Å / 相対比: 1 |
反射 | 解像度: 1.85→15 Å / Num. all: 38461 / Num. obs: 34115 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 7.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.8 |
反射 シェル | 解像度: 1.85→1.92 Å / Rmerge(I) obs: 0.382 / % possible all: 76.5 |
反射 | *PLUS 最低解像度: 15 Å / Num. measured all: 248351 / Rmerge(I) obs: 0.079 |
反射 シェル | *PLUS % possible obs: 76.5 % / Rmerge(I) obs: 0.382 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 1VCB 解像度: 1.85→15 Å / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 1.85→15 Å
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拘束条件 |
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精密化 | *PLUS 最低解像度: 15 Å / Rfactor obs: 0.196 / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.196 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: c_angle_deg / Dev ideal: 1.4 | |||||||||||||||||||||||||
LS精密化 シェル | *PLUS 最高解像度: 1.85 Å / 最低解像度: 1.92 Å / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.248 / Rfactor obs: 0.248 |