+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2cld | ||||||
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タイトル | CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GDP (2) | ||||||
要素 | GTPASE HRASHRAS | ||||||
キーワード | NUCLEOTIDE-BINDING PROTEIN / GUANINE NUCLEOTIDE BINDING PROTEIN (Gタンパク質) / PALMITATE (パルミチン酸) / CAGED GTP / PRENYLATION (プレニル化) / FLUORESCENCE (蛍光) | ||||||
機能・相同性 | 機能・相同性情報 GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / 髄鞘 / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / 低分子量GTPアーゼ / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / cellular response to gamma radiation / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / エンドサイトーシス / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / 走化性 / positive regulation of fibroblast proliferation / 分裂促進因子活性化タンパク質キナーゼ / 細胞老化 / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling 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: 1.22 Å | ||||||
データ登録者 | Klink, B.U. / Goody, R.S. / Scheidig, A.J. | ||||||
引用 | ジャーナル: Biophys.J. / 年: 2006 タイトル: A Newly Designed Microspectrofluorometer for Kinetic Studies on Protein Crystals in Combination with X-Ray Diffraction 著者: Klink, B.U. / Goody, R.S. / Scheidig, A.J. | ||||||
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 | 2cld.cif.gz | 87.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2cld.ent.gz | 67 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2cld.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/cl/2cld ftp://data.pdbj.org/pub/pdb/validation_reports/cl/2cld | 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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1 |
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単位格子 |
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モデル数 | 2 |
-要素
#1: タンパク質 | 分子量: 18859.127 Da / 分子数: 1 / 断片: RESIDUES 1-166 / 変異: YES / 由来タイプ: 組換発現 / 詳細: AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PTAC RAS / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): CK600K / 参照: UniProt: P01112 |
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#2: 化合物 | ChemComp-MG / |
#3: 化合物 | ChemComp-GDP / |
#4: 水 | ChemComp-HOH / |
構成要素の詳細 | RAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED RESIDUE IN CHAIN X, TYR ...RAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED |
-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: 2.2 Å3/Da / 溶媒含有率: 43.5 % |
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結晶化 | 温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.2 詳細: PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.2, 200 MM MAGNESIUM ACETATE, 16% PEG ...詳細: PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.2, 200 MM MAGNESIUM ACETATE, 16% PEG 8000 (FRESHLY PREPARED) MIXTURE OF EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K |
-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: ID14-4 / 波長: 0.939 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2004年12月1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: 0.939 Å / 相対比: 1 |
反射 | 解像度: 1.22→69.34 Å / Num. obs: 47013 / % possible obs: 94.1 % / 冗長度: 6.09 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.5 |
反射 シェル | 解像度: 1.22→1.25 Å / 冗長度: 4.21 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3 / % possible all: 55.5 |
-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: PDB ENTRY 4Q21 解像度: 1.22→69.34 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.111 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. RESIDUES 30-32 ARE DISORDERED. THE CLOSE CONTACTS ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. RESIDUES 30-32 ARE DISORDERED. THE CLOSE CONTACTS WITH WATER MOLECULES ARE CAUSED BY THE TREATMENT OF THE WHOLE PROTEIN CHAIN WITH TWO ALTERNATIVE CONFORMATIONS, BUT ONLY ONE POSITION PER WATER MOLECULE.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 17.04 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.22→69.34 Å
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拘束条件 |
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