+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23977 | |||||||||||||||
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タイトル | Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin | |||||||||||||||
マップデータ | Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 rhodopsin kinase / rhodopsin kinase activity / regulation of opsin-mediated signaling pathway / Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light ...rhodopsin kinase / rhodopsin kinase activity / regulation of opsin-mediated signaling pathway / Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / phototransduction, visible light / thermotaxis / Activation of the phototransduction cascade / detection of temperature stimulus involved in thermoception / outer membrane / arrestin family protein binding / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / regulation of signal transduction / sperm midpiece / 視覚 / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / 遺伝子発現 / protein autophosphorylation / G protein-coupled receptor signaling pathway / ゴルジ体 / シグナル伝達 / zinc ion binding / ATP binding / 生体膜 / identical protein binding / 細胞膜 / 細胞質 類似検索 - 分子機能 | |||||||||||||||
生物種 | Bos taurus (ウシ) / Bovine (ウシ) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.8 Å | |||||||||||||||
データ登録者 | Chen Q / Li Z / Chang L / Tesmer JJG | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Nature / 年: 2021 タイトル: Structures of rhodopsin in complex with G-protein-coupled receptor kinase 1. 著者: Qiuyan Chen / Manolo Plasencia / Zhuang Li / Somnath Mukherjee / Dhabaleswar Patra / Chun-Liang Chen / Thomas Klose / Xin-Qiu Yao / Anthony A Kossiakoff / Leifu Chang / Philip C Andrews / John J G Tesmer / 要旨: G-protein-coupled receptor (GPCR) kinases (GRKs) selectively phosphorylate activated GPCRs, thereby priming them for desensitization. Although it is unclear how GRKs recognize these receptors, a ...G-protein-coupled receptor (GPCR) kinases (GRKs) selectively phosphorylate activated GPCRs, thereby priming them for desensitization. Although it is unclear how GRKs recognize these receptors, a conserved region at the GRK N terminus is essential for this process. Here we report a series of cryo-electron microscopy single-particle reconstructions of light-activated rhodopsin (Rho*) bound to rhodopsin kinase (GRK1), wherein the N terminus of GRK1 forms a helix that docks into the open cytoplasmic cleft of Rho*. The helix also packs against the GRK1 kinase domain and stabilizes it in an active configuration. The complex is further stabilized by electrostatic interactions between basic residues that are conserved in most GPCRs and acidic residues that are conserved in GRKs. We did not observe any density for the regulator of G-protein signalling homology domain of GRK1 or the C terminus of rhodopsin. Crosslinking with mass spectrometry analysis confirmed these results and revealed dynamic behaviour in receptor-bound GRK1 that would allow the phosphorylation of multiple sites in the receptor tail. We have identified GRK1 residues whose mutation augments kinase activity and crosslinking with Rho*, as well as residues that are involved in activation by acidic phospholipids. From these data, we present a general model for how a small family of protein kinases can recognize and be activated by hundreds of different GPCRs. | |||||||||||||||
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_23977.map.gz | 59.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23977-v30.xml emd-23977.xml | 12.3 KB 12.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23977_fsc.xml | 4.6 KB | 表示 | FSCデータファイル |
画像 | emd_23977.png | 48.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23977 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23977 | 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_23977.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.08 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 : Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin
全体 | 名称: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin |
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要素 |
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-超分子 #1: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin
超分子 | 名称: Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 |
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由来(天然) | 生物種: Bos taurus (ウシ) |
-分子 #1: Rhodopsin kinase GRK1
分子 | 名称: Rhodopsin kinase GRK1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: rhodopsin kinase |
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由来(天然) | 生物種: Bos taurus (ウシ) |
分子量 | 理論値: 61.542012 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MDFGELETVV ANSAFIAARG SFDASSGPAS RDRKYLARLK LPPLSKCEAL RESLDLGFEG MCLEQPIGKR LFQQFLRTHE QHGPALQLW KDIEDYDTAD DALRPQKAQA LRAAYLEPQA QLFCSFLDAE TVARARAGAG DGLFQPLLRA VLAHLGQAPF Q EFLDSLYF ...文字列: MDFGELETVV ANSAFIAARG SFDASSGPAS RDRKYLARLK LPPLSKCEAL RESLDLGFEG MCLEQPIGKR LFQQFLRTHE QHGPALQLW KDIEDYDTAD DALRPQKAQA LRAAYLEPQA QLFCSFLDAE TVARARAGAG DGLFQPLLRA VLAHLGQAPF Q EFLDSLYF LRFLQWKWLE AQPMGEDWFL DFRVLGRGGF GEVFACQMKA TGKLYACKKL NKKRLKKRKG YQGAMVEKKI LA KVHSRFI VSLAYAFETK TDLCLVMTIM NGGDIRYHIY NVDEDNPGFQ EPRAIFYTAQ IVSGLEHLHQ RNIIYRDLKP ENV LLDDDG NVRISDLGLA VELKAGQTKT KGYAGTPGFM APELLLGEEY DFSVDYFALG VTLYEMIAAR GPFRARGEKV ENKE LKQRV LEQAVTYPDK FSPASKDFCE ALLQKDPEKR LGFRDGSCDG LRTHPLFRDI SWRQLEAGML TPPFVPDSRT VYAKN IQDV GAFEEVKGVA FEKADTEFFQ EFASGTCPIP WQEEMIETGV FGDLNVWRPD GVDHHHHHH |
-分子 #2: Rhodopsin
分子 | 名称: Rhodopsin / 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: Bovine (ウシ) |
分子量 | 理論値: 39.031457 KDa |
配列 | 文字列: MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFG GFTTTLYTSL HGYFVFGPTG CNLEGFFATL GGEIALWSLV VLAIERYVVV CKPMSNFRFG ENHAIMGVAF T WVMALACA ...文字列: MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFG GFTTTLYTSL HGYFVFGPTG CNLEGFFATL GGEIALWSLV VLAIERYVVV CKPMSNFRFG ENHAIMGVAF T WVMALACA APPLVGWSRY IPEGMQCSCG IDYYTPHEET NNESFVIYMF VVHFIIPLIV IFFCYGQLVF TVKEAAAQQQ ES ATTQKAE KEVTRMVIIM VIAFLICWLP YAGVAFYIFT HQGSDFGPIF MTIPAFFAKT SAVYNPVIYI MMNKQFRNCM VTT LCCGKN PLGDDEASTT VSKTETSQVA PA |
-分子 #3: SANGIVAMYCIN
分子 | 名称: SANGIVAMYCIN / タイプ: ligand / ID: 3 / コピー数: 1 / 式: SGV |
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分子量 | 理論値: 309.278 Da |
Chemical component information | ChemComp-SGV: |
-分子 #4: RETINAL
分子 | 名称: RETINAL / タイプ: ligand / ID: 4 / コピー数: 1 / 式: RET |
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分子量 | 理論値: 284.436 Da |
Chemical component information | ChemComp-RET: |
-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
緩衝液 | pH: 8 |
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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 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 54.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |