+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20612 | |||||||||
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タイトル | GPCR-Beta arrestin structure in lipid bilayer | |||||||||
マップデータ | GPCR-Beta arrestin structure in lipid bilayer | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Muscarinic acetylcholine receptors / symmetric synapse / Golgi Associated Vesicle Biogenesis / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / MAP2K and MAPK activation / Ub-specific processing proteases / G protein-coupled acetylcholine receptor activity / regulation of smooth muscle contraction / 止血 / positive regulation of systemic arterial blood pressure / cholinergic synapse / positive regulation of smooth muscle cell apoptotic process / telencephalon development / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of G protein-coupled receptor signaling pathway / G protein-coupled serotonin receptor activity / arrestin family protein binding / G protein-coupled receptor internalization / response to morphine / Thrombin signalling through proteinase activated receptors (PARs) / regulation of heart contraction / positive regulation of intracellular signal transduction / mitogen-activated protein kinase kinase binding / immunoglobulin complex / positive regulation of Rho protein signal transduction / clathrin binding / stress fiber assembly / negative regulation of Notch signaling pathway / 仮足 / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of receptor internalization / phototransduction / asymmetric synapse / endocytic vesicle / axon terminus / クラスリン / positive regulation of vasoconstriction / cellular response to hormone stimulus / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / activation of adenylate cyclase activity / 視覚 / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / response to cytokine / G protein-coupled receptor binding / nuclear estrogen receptor binding / peptide binding / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / Vasopressin regulates renal water homeostasis via Aquaporins / エンドサイトーシス / protein transport / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / presynaptic membrane / nervous system development / G alpha (i) signalling events / cytoplasmic vesicle / G alpha (s) signalling events / ubiquitin-dependent protein catabolic process / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / 樹状突起スパイン / positive regulation of MAPK cascade 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Rattus norvegicus (ドブネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å | |||||||||
データ登録者 | Staus DP / Hu H / Robertson MJ / Kleinhenz ALW / Wingler LM / Capel WD / Latorraca NR / Lefkowitz RJ / Skiniotis G | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nature / 年: 2020 タイトル: Structure of the M2 muscarinic receptor-β-arrestin complex in a lipid nanodisc. 著者: Dean P Staus / Hongli Hu / Michael J Robertson / Alissa L W Kleinhenz / Laura M Wingler / William D Capel / Naomi R Latorraca / Robert J Lefkowitz / Georgios Skiniotis / 要旨: After activation by an agonist, G-protein-coupled receptors (GPCRs) recruit β-arrestin, which desensitizes heterotrimeric G-protein signalling and promotes receptor endocytosis. Additionally, β- ...After activation by an agonist, G-protein-coupled receptors (GPCRs) recruit β-arrestin, which desensitizes heterotrimeric G-protein signalling and promotes receptor endocytosis. Additionally, β-arrestin directly regulates many cell signalling pathways that can induce cellular responses distinct from that of G proteins. In contrast to G proteins, for which there are many high-resolution structures in complex with GPCRs, the molecular mechanisms underlying the interaction of β-arrestin with GPCRs are much less understood. Here we present a cryo-electron microscopy structure of β-arrestin 1 (βarr1) in complex with M2 muscarinic receptor (M2R) reconstituted in lipid nanodiscs. The M2R-βarr1 complex displays a multimodal network of flexible interactions, including binding of the N domain of βarr1 to phosphorylated receptor residues and insertion of the finger loop of βarr1 into the M2R seven-transmembrane bundle, which adopts a conformation similar to that in the M2R-heterotrimeric G protein complex. Moreover, the cryo-electron microscopy map reveals that the C-edge of βarr1 engages the lipid bilayer. Through atomistic simulations and biophysical, biochemical and cellular assays, we show that the C-edge is critical for stable complex formation, βarr1 recruitment, receptor internalization, and desensitization of G-protein activation. Taken together, these data suggest that the cooperative interactions of β-arrestin with both the receptor and the phospholipid bilayer contribute to its functional versatility. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_20612.map.gz | 49.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20612-v30.xml emd-20612.xml | 18.8 KB 18.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20612.png | 96.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20612 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20612 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_20612.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | GPCR-Beta arrestin structure in lipid bilayer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : Phosphorylated human muscarinic acetylcholine receptor M2 in comp...
全体 | 名称: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30). |
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要素 |
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-超分子 #1: Phosphorylated human muscarinic acetylcholine receptor M2 in comp...
超分子 | 名称: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30). タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 |
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-超分子 #2: Phosphorylated human muscarinic acetylcholine receptor M2
超分子 | 名称: Phosphorylated human muscarinic acetylcholine receptor M2 タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 詳細: Phosphorylated M2R was generated by ligating a synthetic phosphopeptide derived from the vasopressin-2-receptor (V2Rpp) using the enzyme sortase. |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-超分子 #3: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393
超分子 | 名称: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393 タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-超分子 #4: Antibody Fragment (Fab30)
超分子 | 名称: Antibody Fragment (Fab30) / タイプ: complex / ID: 4 / 親要素: 1 / 含まれる分子: #3-#4 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-分子 #1: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera
分子 | 名称: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 56.616176 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: DYKDDDDKNN STNSSNNSLA LTSPYKTFEV VFIVLVAGSL SLVTIIGNIL VMVSIKVNRH LQTVNNYFLF SLACADLIIG VFSMNLYTL YTVIGYWPLG PVVCDLWLAL DYVVSNASVM NLLIISFDRY FCVTKPLTYP VKRTTKMAGM MIAAAWVLSF I LWAPAILF ...文字列: DYKDDDDKNN STNSSNNSLA LTSPYKTFEV VFIVLVAGSL SLVTIIGNIL VMVSIKVNRH LQTVNNYFLF SLACADLIIG VFSMNLYTL YTVIGYWPLG PVVCDLWLAL DYVVSNASVM NLLIISFDRY FCVTKPLTYP VKRTTKMAGM MIAAAWVLSF I LWAPAILF WQFIVGVRTV EDGECYIQFF SNAAVTFGTA IAAFYLPVII MTVLYWHISR ASKSRIKKDK KEPVANQDPV SP SLVQGRI VKPNNNNMPS SDDGLEHNKI QNGKAPRDPV TENCVQGEEK ESSNDSTSVS AVASNMRDDE ITQDENTVST SLG HSKDEN SKQTCIRIGT KTPKSDSCTP TNTTVEVVGS SGQNGDEKQN IVARKIVKMT KQPAKKKPPP SREKKVTRTI LAIL LAFII TWAPYNVMVL INTFCAPCIP NTVWTIGYWL CYINSTINPA CYALCNATFK KTFKHLLMCH YKNIGATRLP ETGGG ARGR TPPSLGPQDE (SEP)C(TPO)(TPO)A(SEP)(SEP)(SEP)LA KDTSS |
-分子 #2: Beta-arrestin-1
分子 | 名称: Beta-arrestin-1 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 45.01718 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: GSPEFPGRLG DKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTVAFR YGREDLDVLG LTFRKDLFV ANVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPSSVTLQP GPEDTGKALG VDYEVKAFVA E NLEEKIHK ...文字列: GSPEFPGRLG DKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTVAFR YGREDLDVLG LTFRKDLFV ANVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPSSVTLQP GPEDTGKALG VDYEVKAFVA E NLEEKIHK RNSVRLVIRK VQYAPERPGP QPTAETTRQF LMSDKPLHLE ASLDKEIYYH GEPISVNVHV TNNTNKTVKK IK ISVRQYA DIVLFNTAQY KVPVAMEEAD DTVAPSSTFS KVYTLTPFLA NNREKRGLAL DGKLKHEDTN LASSTLLREG ANR EILGII VSYKVKVKLV VSRGGLLGDL ASSDVAVELP FTLMHPKPKE EPPHREVPES ETPVDTNLIE LDTNDDDIVF EDFA R |
-分子 #3: Fab30 heavy chain
分子 | 名称: Fab30 heavy chain / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 25.512354 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...文字列: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH |
-分子 #4: Fab30 light chain
分子 | 名称: Fab30 light chain / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 23.435064 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...文字列: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-分子 #5: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1...
分子 | 名称: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide タイプ: ligand / ID: 5 / コピー数: 1 / 式: 2CU |
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分子量 | 理論値: 437.944 Da |
Chemical component information | ChemComp-2CU: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 2 mg/mL |
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緩衝液 | pH: 7.4 |
グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 倍率(補正後): 47169 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 1.2 µm / 倍率(公称値): 47169 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 検出モード: COUNTING / 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 11700000 |
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CTF補正 | ソフトウェア - 名称: Gctf (ver. 1.06) |
初期 角度割当 | タイプ: RANDOM ASSIGNMENT / ソフトウェア - 名称: RELION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.0) / 使用した粒子像数: 145618 |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
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得られたモデル | PDB-6u1n: |