+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2rh1 | |||||||||
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タイトル | High resolution crystal structure of human B2-adrenergic G protein-coupled receptor. | |||||||||
要素 | beta-2-adrenergic receptor/T4-lysozyme chimera | |||||||||
キーワード | MEMBRANE PROTEIN / HYDROLASE / GPCR / 7TM / adrenergic / fusion / lipidic cubic phase / lipidic / mesophase / cholesterol / membrane protein / MEMBRANE PROTEIN - HYDROLASE COMPLEX / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network | |||||||||
機能・相同性 | 機能・相同性情報 beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / positive regulation of autophagosome maturation / norepinephrine binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / positive regulation of autophagosome maturation / norepinephrine binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / neuronal dense core vesicle / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / bone resorption / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / regulation of sodium ion transport / viral release from host cell by cytolysis / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / positive regulation of protein serine/threonine kinase activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / positive regulation of cold-induced thermogenesis / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / lysozyme activity / Clathrin-mediated endocytosis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / lysosome / early endosome / receptor complex / cell surface receptor signaling pathway / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) Enterobacteria phage T4 (ファージ) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å | |||||||||
データ登録者 | Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. ...Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR) | |||||||||
引用 | ジャーナル: Science / 年: 2007 タイトル: High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. 著者: Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. / Stevens, R.C. #1: ジャーナル: To be Published タイトル: GPCR Engineering Yields High-Resolution Structural Insights into beta2 Adrenergic Receptor Function. 著者: Rosenbaum, D.M. / Cherezov, V. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Yao, X.J. / Weis, W.I. / Stevens, R.C. / Kobilka, B.K. | |||||||||
履歴 |
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Remark 600 | HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR ...HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR RESPECTIVE CYSTEINE RESIDUES. | |||||||||
Remark 999 | SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED ...SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED TO ORIGINAL SEQUENCE DATABASE RESIDUE NUMBERS (2-161) OF THE LYSOZYME PART IN COORDINATES TO DISTINGUISH THE LYSOZYME PART IN THE CHAIN. THEREFORE THE RESIDUES OF LYSOZYME PART HAVE NUMBERS A1002-A1161. |
-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 | 2rh1.cif.gz | 115.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2rh1.ent.gz | 84 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2rh1.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
文書・要旨 | 2rh1_validation.pdf.gz | 2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2rh1_full_validation.pdf.gz | 2 MB | 表示 | |
XML形式データ | 2rh1_validation.xml.gz | 12.7 KB | 表示 | |
CIF形式データ | 2rh1_validation.cif.gz | 18.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/rh/2rh1 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/2rh1 | HTTPS FTP |
-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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Components on special symmetry positions |
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詳細 | Authors state that the biological unit is unknown |
-要素
-タンパク質 / 糖 , 2種, 2分子 A
#1: タンパク質 | 分子量: 56601.438 Da / 分子数: 1 / 変異: N187E, C54T, C97A / 由来タイプ: 組換発現 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Enterobacteria phage T4 (ファージ) 属: Homo, T4-like viruses / 生物種: , Enterobacteria phage T4 sensu lato / 株: , 解説: The construct has been obtained by overlapping extension PCR 遺伝子: ADRB2, ADRB2R, B2AR / E / プラスミド: pFastbac1 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P07550, UniProt: P00720 |
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#2: 多糖 | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-非ポリマー , 8種, 63分子
#3: 化合物 | ChemComp-SO4 / #4: 化合物 | ChemComp-CAU / ( | #5: 化合物 | #6: 化合物 | ChemComp-ACM / | #7: 化合物 | #8: 化合物 | ChemComp-PLM / | #9: 化合物 | ChemComp-12P / | #10: 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: 27 |
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-試料調製
結晶 | マシュー密度: 3.07 Å3/Da / 溶媒含有率: 59.98 % 解説: This structure is a part of the Roadmap/PSI community outreach program, not a specific PSI target. |
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結晶化 | 温度: 293 K / 手法: lipidic mesophase / pH: 6.75 詳細: 30-35% v/v PEG 400, 0.1-0.2 M Na2SO4, 0.1 M Bis-tris propane pH 6.5-7.0, 5-7% 1,4-Butanediol, 8-10% Cholesterol, 52-50% Monoolein, pH 6.75, LIPIDIC MESOPHASE, temperature 293K |
-データ収集
回折 |
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放射光源 |
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検出器 |
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放射 | モノクロメーター: Double crystal / 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: 1.03321 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 2.4→20 Å / Num. all: 26705 / Num. obs: 26506 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.908 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.62 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
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-位相決定
位相決定 | 手法: 分子置換 |
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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: 分子置換 開始モデル: PDB entries 1U19, 2LZM 解像度: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.501 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.22 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Water #548 has strong difference density but weak 2Fo-Fc density.
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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: 1.4 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 63.912 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.4→19.95 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.4→2.461 Å / Total num. of bins used: 20
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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